; 2025-04-28.204023
peak-motifs  -v 1 -title TnaA_WD_ALL+ -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,dyads,positions,local_words -nmotifs 10 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db DMMPMM_drosophila tf $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6



; 2025-04-28.204023
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/images_html


; 2025-04-28.204023
$RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifspeak_seq -from fasta -to fasta -mask non-dna | $RSAT/perl-scripts/sub-sequence -origin center -from -500 -to 499 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta


; 2025-04-28.204023
$RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -ml 40 -mis 3 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta


; 2025-04-28.204024
$RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_seqlen_distrib.tab


; 2025-04-28.204024
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; TnaA_WD_ALL+' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_seqlen_distrib.tab -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_seqlen_distrib.png


; 2025-04-28.204024
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab_time.txt $RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -l 1 -1str -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab


; 2025-04-28.204024
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png


; 2025-04-28.204024
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab_time.txt $RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -l 2 -1str -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab


; 2025-04-28.204024
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -digits 3 -out_format png -col_width 50 -rownames -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png


; 2025-04-28.204025
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 1 -ci 20 -img_format png -title 'TnaA_WD_ALL+' -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab


; 2025-04-28.204026
grep -v ";" $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-5 -xgstep2 20 -vline '#666666' 0 -xsize 700 -ysize 250 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/1nt-1str_colors.tab -title 'Nucleotide composition profiles; test sequence; TnaA_WD_ALL+' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png


; 2025-04-28.204026
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title 'TnaA_WD_ALL+' -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab


; 2025-04-28.204029
grep -v ";" $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab | cut -f 1,10-10000 | $RSAT/perl-scripts/transpose-table | $RSAT/perl-scripts/XYgraph -xcol 1 -ycol 2-17 -xgstep2 20 -vline '#666666' 0 -xsize 700 -ysize 250 -format png -legend -lines -pointsize 0 -legend -header -colors $RSAT/perl-scripts/lib/color_palettes/2nt-1str_colors.tab -title 'Dinucleotide composition profiles; test sequence; TnaA_WD_ALL+' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png


; 2025-04-28.204029
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.tab_time.txt $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -markov 2 -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.tab


; 2025-04-28.204029
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.tab -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 10 -max_asmb_width 20 -subst 1 -prefix oligos_6nt_mkv2 -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm


; 2025-04-28.204035
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.tab_time.txt $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 7 -markov 2 -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.tab


; 2025-04-28.204036
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.tab -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 10 -max_asmb_width 20 -subst 1 -prefix oligos_7nt_mkv2 -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm


; 2025-04-28.204042
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab_time.txt $RSAT/perl-scripts/dyad-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -quick -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,ratio,zscore,rank -2str -noov -seqtype dna -l 3 -sp 0-20  -bg monads -pseudo 0.01 | perl -pe 's/n\{0\}//g' >$RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab


; 2025-04-28.204046
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 10 -max_asmb_width 20 -subst 0 -prefix dyads -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm


; 2025-04-28.204058
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return chi,sig,rank,distrib,index -max_graphs 100 -2str -noov -seqtype dna -l 6 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'TnaA_WD_ALL+' -origin center -offset 0 -max_graphs 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab


; 2025-04-28.204059
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 10 -max_asmb_width 20 -subst 1 -prefix positions_6nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm


; 2025-04-28.204101
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return chi,sig,rank,distrib,index -max_graphs 100 -2str -noov -seqtype dna -l 7 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'TnaA_WD_ALL+' -origin center -offset 0 -max_graphs 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab


; 2025-04-28.204104
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 10 -max_asmb_width 20 -subst 1 -prefix positions_7nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm


; 2025-04-28.204106
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_6nt/peak-motifs_local_words-2str-noov_6nt_windgroup50.tab_time.txt $RSAT/python-scripts/local-word-analysis -v 3 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta --min=occ_sig 0 --sort=-occ_sig --max=rank 100 --max=w_rank 1 +- --center=0 --windowgroup=50 --len 6 > $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_6nt/peak-motifs_local_words-2str-noov_6nt_windgroup50.tab


; 2025-04-28.204106
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_6nt/peak-motifs_local_words-2str-noov_6nt_windgroup50_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_6nt/peak-motifs_local_words-2str-noov_6nt_windgroup50.tab -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 10 -max_asmb_width 20 -subst 1 -prefix local_words_6nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_6nt/peak-motifs_local_words-2str-noov_6nt_windgroup50_pssm


; 2025-04-28.204106
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_7nt/peak-motifs_local_words-2str-noov_7nt_windgroup50.tab_time.txt $RSAT/python-scripts/local-word-analysis -v 3 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta --min=occ_sig 0 --sort=-occ_sig --max=rank 100 --max=w_rank 1 +- --center=0 --windowgroup=50 --len 7 > $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_7nt/peak-motifs_local_words-2str-noov_7nt_windgroup50.tab


; 2025-04-28.204106
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_7nt/peak-motifs_local_words-2str-noov_7nt_windgroup50_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_7nt/peak-motifs_local_words-2str-noov_7nt_windgroup50.tab -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 10 -max_asmb_width 20 -subst 1 -prefix local_words_7nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/local_words_7nt/peak-motifs_local_words-2str-noov_7nt_windgroup50_pssm


; 2025-04-28.204106
rm -f $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_discovered.tf


; 2025-04-28.204106
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1.tab


; 2025-04-28.204107
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2.tab


; 2025-04-28.204107
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.tab


; 2025-04-28.204107
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4.tab


; 2025-04-28.204107
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5.tab


; 2025-04-28.204107
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6.tab


; 2025-04-28.204107
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7.tab


; 2025-04-28.204108
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8.tab


; 2025-04-28.204108
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9.tab


; 2025-04-28.204108
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10.tab


; 2025-04-28.204108
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tab


; 2025-04-28.204108
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tab


; 2025-04-28.204108
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tab


; 2025-04-28.204108
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.tab


; 2025-04-28.204108
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3.tab


; 2025-04-28.204109
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4.tab


; 2025-04-28.204109
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.tab


; 2025-04-28.204109
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6.tab


; 2025-04-28.204109
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7.tab


; 2025-04-28.204109
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8.tab


; 2025-04-28.204109
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9.tab


; 2025-04-28.204109
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10.tab


; 2025-04-28.204110
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tab


; 2025-04-28.204110
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tab


; 2025-04-28.204110
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tab


; 2025-04-28.204110
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tab


; 2025-04-28.204110
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tab


; 2025-04-28.204110
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tab


; 2025-04-28.204110
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tab


; 2025-04-28.204111
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6.tab


; 2025-04-28.204111
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7.tab


; 2025-04-28.204111
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8.tab


; 2025-04-28.204111
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9.tab


; 2025-04-28.204111
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10.tab


; 2025-04-28.204111
$RSAT/perl-scripts/compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab; $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_disco_compa.html


; 2025-04-28.204213
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml


; 2025-04-28.204214
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_vs_db_DMMPMM_drosophila


; 2025-04-28.204214
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_vs_db_DMMPMM_drosophila


; 2025-04-28.204215
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_vs_db_DMMPMM_drosophila


; 2025-04-28.204215
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_vs_db_DMMPMM_drosophila


; 2025-04-28.204216
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_vs_db_DMMPMM_drosophila


; 2025-04-28.204217
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_vs_db_DMMPMM_drosophila


; 2025-04-28.204218
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_vs_db_DMMPMM_drosophila


; 2025-04-28.204218
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_vs_db_DMMPMM_drosophila


; 2025-04-28.204219
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_vs_db_DMMPMM_drosophila


; 2025-04-28.204221
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_vs_db_DMMPMM_drosophila


; 2025-04-28.204221
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_DMMPMM_drosophila


; 2025-04-28.204221
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_DMMPMM_drosophila


; 2025-04-28.204222
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_DMMPMM_drosophila


; 2025-04-28.204222
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_DMMPMM_drosophila


; 2025-04-28.204223
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_vs_db_DMMPMM_drosophila


; 2025-04-28.204223
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_vs_db_DMMPMM_drosophila


; 2025-04-28.204223
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_DMMPMM_drosophila


; 2025-04-28.204225
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_vs_db_DMMPMM_drosophila


; 2025-04-28.204225
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_vs_db_DMMPMM_drosophila


; 2025-04-28.204226
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_vs_db_DMMPMM_drosophila


; 2025-04-28.204226
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_vs_db_DMMPMM_drosophila


; 2025-04-28.204226
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_vs_db_DMMPMM_drosophila


; 2025-04-28.204228
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_DMMPMM_drosophila


; 2025-04-28.204228
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_DMMPMM_drosophila


; 2025-04-28.204229
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_DMMPMM_drosophila


; 2025-04-28.204229
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_DMMPMM_drosophila


; 2025-04-28.204230
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_DMMPMM_drosophila


; 2025-04-28.204230
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_DMMPMM_drosophila


; 2025-04-28.204231
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_DMMPMM_drosophila


; 2025-04-28.204231
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_vs_db_DMMPMM_drosophila


; 2025-04-28.204232
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_vs_db_DMMPMM_drosophila


; 2025-04-28.204232
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_vs_db_DMMPMM_drosophila


; 2025-04-28.204233
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_vs_db_DMMPMM_drosophila


; 2025-04-28.204233
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_vs_db_DMMPMM_drosophila


; 2025-04-28.204233
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab_time.txt $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab


; 2025-04-28.204243
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.gml


; 2025-04-28.204244
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab


; 2025-04-28.204244
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_site_distrib.tab


; 2025-04-28.204244
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_site_distrib.png


; 2025-04-28.204244
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites_per_peak.tab


; 2025-04-28.204245
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites_per_peak.png


; 2025-04-28.204245
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab


; 2025-04-28.204245
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_site_distrib.tab


; 2025-04-28.204245
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_site_distrib.png


; 2025-04-28.204245
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites_per_peak.tab


; 2025-04-28.204245
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites_per_peak.png


; 2025-04-28.204246
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab


; 2025-04-28.204246
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_site_distrib.tab


; 2025-04-28.204246
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m3' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_site_distrib.png


; 2025-04-28.204246
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites_per_peak.tab


; 2025-04-28.204246
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m3' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites_per_peak.png


; 2025-04-28.204246
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites.tab


; 2025-04-28.204247
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_site_distrib.tab


; 2025-04-28.204247
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m4' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_site_distrib.png


; 2025-04-28.204247
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites_per_peak.tab


; 2025-04-28.204247
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m4' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites_per_peak.png


; 2025-04-28.204247
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites.tab


; 2025-04-28.204247
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_site_distrib.tab


; 2025-04-28.204248
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m5' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_site_distrib.png


; 2025-04-28.204248
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites_per_peak.tab


; 2025-04-28.204248
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m5' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites_per_peak.png


; 2025-04-28.204248
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites.tab


; 2025-04-28.204248
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_site_distrib.tab


; 2025-04-28.204248
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m6' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_site_distrib.png


; 2025-04-28.204249
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites_per_peak.tab


; 2025-04-28.204249
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m6' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites_per_peak.png


; 2025-04-28.204249
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites.tab


; 2025-04-28.204249
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_site_distrib.tab


; 2025-04-28.204249
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m7' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_site_distrib.png


; 2025-04-28.204249
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites_per_peak.tab


; 2025-04-28.204249
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m7' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites_per_peak.png


; 2025-04-28.204250
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites.tab


; 2025-04-28.204250
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_site_distrib.tab


; 2025-04-28.204250
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m8' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_site_distrib.png


; 2025-04-28.204250
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites_per_peak.tab


; 2025-04-28.204250
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m8' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites_per_peak.png


; 2025-04-28.204250
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites.tab


; 2025-04-28.204251
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_site_distrib.tab


; 2025-04-28.204251
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m9' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_site_distrib.png


; 2025-04-28.204251
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites_per_peak.tab


; 2025-04-28.204251
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m9' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites_per_peak.png


; 2025-04-28.204251
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites.tab


; 2025-04-28.204252
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_site_distrib.tab


; 2025-04-28.204252
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_mkv2_m10' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_site_distrib.png


; 2025-04-28.204252
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites_per_peak.tab


; 2025-04-28.204252
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_mkv2_m10' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites_per_peak.png


; 2025-04-28.204252
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab


; 2025-04-28.204252
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab


; 2025-04-28.204253
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_site_distrib.png


; 2025-04-28.204253
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab


; 2025-04-28.204253
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_6nt_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites_per_peak.png


; 2025-04-28.204253
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab


; 2025-04-28.204253
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab


; 2025-04-28.204253
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_site_distrib.png


; 2025-04-28.204254
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab


; 2025-04-28.204254
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_6nt_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites_per_peak.png


; 2025-04-28.204254
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab


; 2025-04-28.204254
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_site_distrib.tab


; 2025-04-28.204254
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_site_distrib.png


; 2025-04-28.204254
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites_per_peak.tab


; 2025-04-28.204255
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites_per_peak.png


; 2025-04-28.204255
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab


; 2025-04-28.204255
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_site_distrib.tab


; 2025-04-28.204255
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_site_distrib.png


; 2025-04-28.204255
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites_per_peak.tab


; 2025-04-28.204255
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites_per_peak.png


; 2025-04-28.204256
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites.tab


; 2025-04-28.204256
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_site_distrib.tab


; 2025-04-28.204256
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m3' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_site_distrib.png


; 2025-04-28.204256
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites_per_peak.tab


; 2025-04-28.204256
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m3' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites_per_peak.png


; 2025-04-28.204256
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites.tab


; 2025-04-28.204257
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_site_distrib.tab


; 2025-04-28.204257
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m4' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_site_distrib.png


; 2025-04-28.204257
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites_per_peak.tab


; 2025-04-28.204257
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m4' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites_per_peak.png


; 2025-04-28.204257
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites.tab


; 2025-04-28.204258
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_site_distrib.tab


; 2025-04-28.204258
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m5' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_site_distrib.png


; 2025-04-28.204258
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites_per_peak.tab


; 2025-04-28.204258
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m5' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites_per_peak.png


; 2025-04-28.204258
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites.tab


; 2025-04-28.204258
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_site_distrib.tab


; 2025-04-28.204259
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m6' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_site_distrib.png


; 2025-04-28.204259
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites_per_peak.tab


; 2025-04-28.204259
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m6' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites_per_peak.png


; 2025-04-28.204259
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites.tab


; 2025-04-28.204259
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_site_distrib.tab


; 2025-04-28.204259
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m7' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_site_distrib.png


; 2025-04-28.204300
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites_per_peak.tab


; 2025-04-28.204300
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m7' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites_per_peak.png


; 2025-04-28.204300
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites.tab


; 2025-04-28.204300
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_site_distrib.tab


; 2025-04-28.204300
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m8' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_site_distrib.png


; 2025-04-28.204300
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites_per_peak.tab


; 2025-04-28.204300
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m8' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites_per_peak.png


; 2025-04-28.204301
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites.tab


; 2025-04-28.204301
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_site_distrib.tab


; 2025-04-28.204301
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m9' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_site_distrib.png


; 2025-04-28.204301
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites_per_peak.tab


; 2025-04-28.204301
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m9' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites_per_peak.png


; 2025-04-28.204301
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites.tab


; 2025-04-28.204302
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_site_distrib.tab


; 2025-04-28.204302
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_mkv2_m10' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_site_distrib.png


; 2025-04-28.204302
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites_per_peak.tab


; 2025-04-28.204302
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_mkv2_m10' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites_per_peak.png


; 2025-04-28.204302
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab


; 2025-04-28.204303
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab


; 2025-04-28.204303
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_site_distrib.png


; 2025-04-28.204303
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab


; 2025-04-28.204303
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_7nt_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites_per_peak.png


; 2025-04-28.204303
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab


; 2025-04-28.204303
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab


; 2025-04-28.204303
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_site_distrib.png


; 2025-04-28.204304
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab


; 2025-04-28.204304
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : positions_7nt_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites_per_peak.png


; 2025-04-28.204304
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab


; 2025-04-28.204304
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab


; 2025-04-28.204304
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.png


; 2025-04-28.204304
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab


; 2025-04-28.204304
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m1' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.png


; 2025-04-28.204305
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab


; 2025-04-28.204305
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab


; 2025-04-28.204305
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.png


; 2025-04-28.204305
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab


; 2025-04-28.204305
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m2' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.png


; 2025-04-28.204305
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab


; 2025-04-28.204306
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.tab


; 2025-04-28.204306
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m3' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.png


; 2025-04-28.204306
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.tab


; 2025-04-28.204306
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m3' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.png


; 2025-04-28.204306
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab


; 2025-04-28.204307
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_site_distrib.tab


; 2025-04-28.204307
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m4' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_site_distrib.png


; 2025-04-28.204307
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_per_peak.tab


; 2025-04-28.204307
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m4' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_per_peak.png


; 2025-04-28.204307
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab


; 2025-04-28.204307
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_site_distrib.tab


; 2025-04-28.204308
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m5' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_site_distrib.png


; 2025-04-28.204308
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_per_peak.tab


; 2025-04-28.204308
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m5' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_per_peak.png


; 2025-04-28.204308
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites.tab


; 2025-04-28.204308
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_site_distrib.tab


; 2025-04-28.204308
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m6' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_site_distrib.png


; 2025-04-28.204308
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites_per_peak.tab


; 2025-04-28.204309
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m6' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites_per_peak.png


; 2025-04-28.204309
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites.tab


; 2025-04-28.204309
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_site_distrib.tab


; 2025-04-28.204309
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m7' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_site_distrib.png


; 2025-04-28.204309
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites_per_peak.tab


; 2025-04-28.204310
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m7' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites_per_peak.png


; 2025-04-28.204310
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites.tab


; 2025-04-28.204310
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_site_distrib.tab


; 2025-04-28.204310
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m8' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_site_distrib.png


; 2025-04-28.204310
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites_per_peak.tab


; 2025-04-28.204310
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m8' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites_per_peak.png


; 2025-04-28.204311
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites.tab


; 2025-04-28.204311
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_site_distrib.tab


; 2025-04-28.204311
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m9' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_site_distrib.png


; 2025-04-28.204311
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites_per_peak.tab


; 2025-04-28.204311
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m9' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites_per_peak.png


; 2025-04-28.204311
time -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites.tab


; 2025-04-28.204312
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_site_distrib.tab


; 2025-04-28.204312
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : dyads_m10' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_site_distrib.png


; 2025-04-28.204312
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites_per_peak.tab


; 2025-04-28.204312
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : dyads_m10' -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites_per_peak.png


; 2025-04-28.204312
cat $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/peak-motifs_oligos_6nt_mkv2_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/peak-motifs_oligos_6nt_mkv2_m7_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/peak-motifs_oligos_6nt_mkv2_m8_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/peak-motifs_oligos_6nt_mkv2_m9_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/peak-motifs_oligos_6nt_mkv2_m10_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/peak-motifs_oligos_7nt_mkv2_m6_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/peak-motifs_oligos_7nt_mkv2_m8_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/peak-motifs_oligos_7nt_mkv2_m9_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/peak-motifs_oligos_7nt_mkv2_m10_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_sites.tab $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites.tab > $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/sites/peak-motifs_all_motifs_seqcoord.tab


; 2025-04-28.204313
$RSAT/perl-scripts/text-to-html -font variable -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/reports/peak-motifs_timelog.txt -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/reports/peak-motifs_timelog.html

; peak-motifs  -v 1 -title TnaA_WD_ALL+ -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,dyads,positions,local_words -nmotifs 10 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db DMMPMM_drosophila tf $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6
; Program version       	1.256
; Parameter values
;	seq_format            	fasta
;	img_format            	png
;	ref_motifs_format     	transfac
;	purge_match_length    	40
;	purge_mismatches      	3
;	origin                	center
;	offset                	0
;	profiles_ci           	20
;	profiles_max_graphs   	20
;	profiles_strand       	-1str
;	composition_oligo_lengths	1,2
;	profiles_noov         	-ovlp
;	strand                	-2str
;	disco_noov            	-noov
;	oligo_min_len         	6
;	oligo_max_len         	7
;	patterns_max_rank     	100
;	min_ratio             	1
;	min_zscore            	6
;	min_sig               	0
;	oligo_min_mkv         	2
;	oligo_max_mkv         	2
;	under_represented     	0
;	positions_max_graphs  	20
;	asmb_toppat           	100
;	max_asmb_width        	20
;	matrix_nmotifs        	10
; Input files
;	motif_db_DMMPMM_drosophila	/var/www/html/rsat/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf
;	test_seq              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifspeak_seq
; Directories
;	output                        	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/
;	oligos_6nt_mkv2_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/
;	oligos_6nt_mkv2_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/
;	oligos_6nt_mkv2_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/
;	oligos_6nt_mkv2_m4            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/
;	oligos_6nt_mkv2_m5            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/
;	oligos_6nt_mkv2_m6            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/
;	oligos_6nt_mkv2_m7            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/
;	oligos_6nt_mkv2_m8            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/
;	oligos_6nt_mkv2_m9            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/
;	oligos_6nt_mkv2_m10           	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/
;	positions_6nt_m1              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/
;	positions_6nt_m2              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/
;	oligos_7nt_mkv2_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/
;	oligos_7nt_mkv2_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/
;	oligos_7nt_mkv2_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/
;	oligos_7nt_mkv2_m4            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/
;	oligos_7nt_mkv2_m5            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/
;	oligos_7nt_mkv2_m6            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/
;	oligos_7nt_mkv2_m7            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/
;	oligos_7nt_mkv2_m8            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/
;	oligos_7nt_mkv2_m9            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/
;	oligos_7nt_mkv2_m10           	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/
;	positions_7nt_m1              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/
;	positions_7nt_m2              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/
;	dyads_m1                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/
;	dyads_m2                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/
;	dyads_m3                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/
;	dyads_m4                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/
;	dyads_m5                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/
;	dyads_m6                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/
;	dyads_m7                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/
;	dyads_m8                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/
;	dyads_m9                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/
;	dyads_m10                     	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/
; Output files
;	1nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab
;	2nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab
;	archive                       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_archive.zip
;	dyads                         	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_2pssm                   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt
;	dyads_asmb                    	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
;	dyads_m10_logo                	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_logo.png
;	dyads_m10_logo_rc             	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_logo_rc.png
;	dyads_m10_pssm_enrichment     	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_scan_mkv1_enrichment.tab
;	dyads_m10_pssm_enrichment_png 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_scan_mkv1_enrichment.png
;	dyads_m10_pssm_site_distrib   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_site_distrib.tab
;	dyads_m10_pssm_site_distrib_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_site_distrib.png
;	dyads_m10_pssm_sites          	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites.tab
;	dyads_m10_pssm_sites_per_peak 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites_per_peak.tab
;	dyads_m10_pssm_sites_per_peak_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_sites_per_peak.png
;	dyads_m10_tab                 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10.tab
;	dyads_m10_tf                  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10.tf
;	dyads_m10_vs_db_DMMPMM_drosophila	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_vs_db_DMMPMM_drosophila.tab
;	dyads_m10_vs_db_DMMPMM_drosophila_html	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_vs_db_DMMPMM_drosophila.html
;	dyads_m10_vs_ref              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_vs_ref.tab
;	dyads_m10_vs_ref_html         	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/peak-motifs_dyads_m10_vs_ref.html
;	dyads_m1_logo                 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_logo.png
;	dyads_m1_logo_rc              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_logo_rc.png
;	dyads_m1_pssm_enrichment      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.tab
;	dyads_m1_pssm_enrichment_png  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.png
;	dyads_m1_pssm_site_distrib    	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab
;	dyads_m1_pssm_site_distrib_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.png
;	dyads_m1_pssm_sites           	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab
;	dyads_m1_pssm_sites_per_peak  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab
;	dyads_m1_pssm_sites_per_peak_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.png
;	dyads_m1_tab                  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tab
;	dyads_m1_tf                   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf
;	dyads_m1_vs_db_DMMPMM_drosophila	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_DMMPMM_drosophila.tab
;	dyads_m1_vs_db_DMMPMM_drosophila_html	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_DMMPMM_drosophila.html
;	dyads_m1_vs_ref               	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_ref.tab
;	dyads_m1_vs_ref_html          	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_ref.html
;	dyads_m2_logo                 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_logo.png
;	dyads_m2_logo_rc              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_logo_rc.png
;	dyads_m2_pssm_enrichment      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.tab
;	dyads_m2_pssm_enrichment_png  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.png
;	dyads_m2_pssm_site_distrib    	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab
;	dyads_m2_pssm_site_distrib_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.png
;	dyads_m2_pssm_sites           	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab
;	dyads_m2_pssm_sites_per_peak  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab
;	dyads_m2_pssm_sites_per_peak_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.png
;	dyads_m2_tab                  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tab
;	dyads_m2_tf                   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf
;	dyads_m2_vs_db_DMMPMM_drosophila	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_DMMPMM_drosophila.tab
;	dyads_m2_vs_db_DMMPMM_drosophila_html	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_DMMPMM_drosophila.html
;	dyads_m2_vs_ref               	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_ref.tab
;	dyads_m2_vs_ref_html          	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_ref.html
;	dyads_m3_logo                 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_logo.png
;	dyads_m3_logo_rc              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_logo_rc.png
;	dyads_m3_pssm_enrichment      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.tab
;	dyads_m3_pssm_enrichment_png  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.png
;	dyads_m3_pssm_site_distrib    	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.tab
;	dyads_m3_pssm_site_distrib_graph	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.png
;	dyads_m3_pssm_sites           	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab
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;	positions_7nt_pssm_logo_rc2   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m2_rc.png
;	positions_7nt_pssm_logo_rc3   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3_rc.png
;	positions_7nt_pssm_logo_rc4   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m4_rc.png
;	positions_7nt_pssm_logo_rc5   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m5_rc.png
;	positions_7nt_pssm_logo_rc6   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m6_rc.png
;	positions_7nt_pssm_logo_rc7   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m7_rc.png
;	positions_7nt_pssm_logo_rc8   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m8_rc.png
;	positions_7nt_pssm_logo_rc9   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m9_rc.png
;	positions_7nt_pssm_sig        	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf
;	positions_7nt_pssm_tf         	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf
;	small_summary                 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_small_summary.html
;	small_summary_txt             	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/reports/peak-motifs_small_summary.txt
;	synthesis                     	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_synthesis.html
;	test_converted                	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta
;	test_purged                   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta
;	test_seqlen                   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_seqlen.tab
;	test_seqlen_distrib           	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_seqlen_distrib.png
;	timelog                       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/reports/peak-motifs_timelog.txt
;	timelog_html                  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/reports/peak-motifs_timelog.html
;	timetable                     	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/reports/peak-motifs_timetable.txt

; 2025-04-28.204313
(cd $RSAT/public_html/tmp/www-data/2025/04/28 ;  zip -ryq peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_archive.zip peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6 -x peak-motifs_archive.zip)


; 2025-04-28.204313
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/images_html

; peak-motifs  -v 1 -title TnaA_WD_ALL+ -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,dyads,positions,local_words -nmotifs 10 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db DMMPMM_drosophila tf $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6
; Program version       	1.256
; Parameter values
;	seq_format            	fasta
;	img_format            	png
;	ref_motifs_format     	transfac
;	purge_match_length    	40
;	purge_mismatches      	3
;	origin                	center
;	offset                	0
;	profiles_ci           	20
;	profiles_max_graphs   	20
;	profiles_strand       	-1str
;	composition_oligo_lengths	1,2
;	profiles_noov         	-ovlp
;	strand                	-2str
;	disco_noov            	-noov
;	oligo_min_len         	6
;	oligo_max_len         	7
;	patterns_max_rank     	100
;	min_ratio             	1
;	min_zscore            	6
;	min_sig               	0
;	oligo_min_mkv         	2
;	oligo_max_mkv         	2
;	under_represented     	0
;	positions_max_graphs  	20
;	asmb_toppat           	100
;	max_asmb_width        	20
;	matrix_nmotifs        	10
; Input files
;	motif_db_DMMPMM_drosophila	/var/www/html/rsat/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf
;	test_seq              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifspeak_seq
; Directories
;	output                        	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/
;	oligos_6nt_mkv2_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m1/
;	oligos_6nt_mkv2_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m2/
;	oligos_6nt_mkv2_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m3/
;	oligos_6nt_mkv2_m4            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m4/
;	oligos_6nt_mkv2_m5            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m5/
;	oligos_6nt_mkv2_m6            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m6/
;	oligos_6nt_mkv2_m7            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m7/
;	oligos_6nt_mkv2_m8            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m8/
;	oligos_6nt_mkv2_m9            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m9/
;	oligos_6nt_mkv2_m10           	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_6nt_mkv2_m10/
;	positions_6nt_m1              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m1/
;	positions_6nt_m2              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_6nt_m2/
;	oligos_7nt_mkv2_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m1/
;	oligos_7nt_mkv2_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m2/
;	oligos_7nt_mkv2_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m3/
;	oligos_7nt_mkv2_m4            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m4/
;	oligos_7nt_mkv2_m5            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m5/
;	oligos_7nt_mkv2_m6            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m6/
;	oligos_7nt_mkv2_m7            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m7/
;	oligos_7nt_mkv2_m8            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m8/
;	oligos_7nt_mkv2_m9            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m9/
;	oligos_7nt_mkv2_m10           	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/oligos_7nt_mkv2_m10/
;	positions_7nt_m1              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m1/
;	positions_7nt_m2              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/
;	dyads_m1                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m1/
;	dyads_m2                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m2/
;	dyads_m3                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m3/
;	dyads_m4                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m4/
;	dyads_m5                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m5/
;	dyads_m6                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m6/
;	dyads_m7                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m7/
;	dyads_m8                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m8/
;	dyads_m9                      	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m9/
;	dyads_m10                     	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/dyads_m10/
; Output files
;	1nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab
;	2nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab
;	archive                       	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_archive.zip
;	dyads                         	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_2pssm                   	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt
;	dyads_asmb                    	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
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;	positions_7nt_m2_vs_db_DMMPMM_drosophila	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_DMMPMM_drosophila.tab
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;	test_converted                	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/data/sequences/peak-motifs_test_maxlen1000.fasta
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;	timelog_html                  	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/reports/peak-motifs_timelog.html
;	timetable                     	/var/www/html/rsat/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/reports/peak-motifs_timetable.txt

; 2025-04-28.204314
(cd $RSAT/public_html/tmp/www-data/2025/04/28 ;  zip -ryq peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_archive.zip peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_synthesis.html -x peak-motifs_archive.zip)


; 2025-04-28.204314
$RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/reports/peak-motifs_small_summary.txt -no_sort  -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_small_summary.html


; 2025-04-28.204314
(cd $RSAT/public_html/tmp/www-data/2025/04/28 ;  zip -ryq peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_archive.zip peak-motifs.2025-04-28.204023_2025-04-28.204023_gX3AM6/peak-motifs_small_summary.html -x peak-motifs_archive.zip)

; Host name	rsat
; Job started	2025-04-28.204023
; Job done	2025-04-28.204314
; Seconds	0.52
;	user	0.52
;	system	0.89
;	cuser	148.6
;	csystem	26.17