; 2025-05-21.033914
peak-motifs  -v 1 -title MEyellowgreen -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifspeak_seq -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -offset 200 -motif_db footprintDB-plants tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2



; 2025-05-21.033914
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/images_html


; 2025-05-21.033914
$RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifspeak_seq -from fasta -to fasta -mask non-dna -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta


; 2025-05-21.033914
$RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -ml 40 -mis 3 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta


; 2025-05-21.033914
$RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_seqlen_distrib.tab


; 2025-05-21.033915
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; MEyellowgreen' -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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_seqlen_distrib.tab -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_seqlen_distrib.png


; 2025-05-21.033915
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta -l 1 -1str -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab


; 2025-05-21.033915
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png


; 2025-05-21.033915
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta -l 2 -1str -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab


; 2025-05-21.033915
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png


; 2025-05-21.033915
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_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 'MEyellowgreen' -origin center -offset 200 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab


; 2025-05-21.033917
grep -v ";" $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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; MEyellowgreen' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png


; 2025-05-21.033917
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_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 'MEyellowgreen' -origin center -offset 200 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab


; 2025-05-21.033920
grep -v ";" $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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; MEyellowgreen' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png


; 2025-05-21.033920
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.tab


; 2025-05-21.033920
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.tab -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm


; 2025-05-21.033922
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.tab


; 2025-05-21.033924
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.tab -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm


; 2025-05-21.033925
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2.tab_time.txt $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_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 8 -markov 2 -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2.tab


; 2025-05-21.033929
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2.tab -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_8nt_mkv2 -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2_pssm


; 2025-05-21.033931
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab_time.txt $RSAT/perl-scripts/dyad-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta -quick -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,ratio,zscore,rank -2str -noov -seqtype dna -l 3 -sp 0-20  -bg monads -pseudo 0.01 | perl -pe 's/n\{0\}//g' >$RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab


; 2025-05-21.033936
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm


; 2025-05-21.033939
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_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 'MEyellowgreen' -origin center -offset 200 -max_graphs 20 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab


; 2025-05-21.033940
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm


; 2025-05-21.033940
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_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 'MEyellowgreen' -origin center -offset 200 -max_graphs 20 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab


; 2025-05-21.033943
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm


; 2025-05-21.033943
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta -format fasta -sort  -return chi,sig,rank,distrib,index -max_graphs 100 -2str -noov -seqtype dna -l 8 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'MEyellowgreen' -origin center -offset 200 -max_graphs 20 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab


; 2025-05-21.033950
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -pl $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix positions_8nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm


; 2025-05-21.033950
rm -f $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_discovered.tf


; 2025-05-21.033950
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1.tab


; 2025-05-21.033950
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2.tab


; 2025-05-21.033951
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.tab


; 2025-05-21.033951
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tab


; 2025-05-21.033951
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.tab


; 2025-05-21.033951
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1.tab


; 2025-05-21.033951
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2.tab


; 2025-05-21.033951
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3.tab


; 2025-05-21.033951
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4.tab


; 2025-05-21.033951
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5.tab


; 2025-05-21.033952
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tab


; 2025-05-21.033952
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tab


; 2025-05-21.033952
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tab


; 2025-05-21.033952
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tab


; 2025-05-21.033952
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tab


; 2025-05-21.033952
$RSAT/perl-scripts/compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab; $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_disco_compa.html


; 2025-05-21.033959
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml


; 2025-05-21.034000
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_vs_db_footprintDB-plants


; 2025-05-21.034001
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_vs_db_footprintDB-plants


; 2025-05-21.034003
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_vs_db_footprintDB-plants


; 2025-05-21.034005
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_footprintDB-plants


; 2025-05-21.034007
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_footprintDB-plants


; 2025-05-21.034008
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_vs_db_footprintDB-plants


; 2025-05-21.034010
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_vs_db_footprintDB-plants


; 2025-05-21.034012
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_vs_db_footprintDB-plants


; 2025-05-21.034014
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_vs_db_footprintDB-plants


; 2025-05-21.034015
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_vs_db_footprintDB-plants


; 2025-05-21.034017
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_footprintDB-plants


; 2025-05-21.034019
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB-plants


; 2025-05-21.034021
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB-plants


; 2025-05-21.034022
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB-plants


; 2025-05-21.034024
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants


; 2025-05-21.034026
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab_time.txt $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab


; 2025-05-21.034030
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.gml


; 2025-05-21.034130
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab


; 2025-05-21.034130
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_site_distrib.tab


; 2025-05-21.034130
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_site_distrib.png


; 2025-05-21.034131
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites_per_peak.tab


; 2025-05-21.034131
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites_per_peak.png


; 2025-05-21.034131
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab


; 2025-05-21.034131
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_site_distrib.tab


; 2025-05-21.034131
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_site_distrib.png


; 2025-05-21.034131
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites_per_peak.tab


; 2025-05-21.034131
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites_per_peak.png


; 2025-05-21.034132
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab


; 2025-05-21.034132
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_site_distrib.tab


; 2025-05-21.034132
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_site_distrib.png


; 2025-05-21.034132
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites_per_peak.tab


; 2025-05-21.034132
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites_per_peak.png


; 2025-05-21.034132
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab


; 2025-05-21.034133
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_site_distrib.tab


; 2025-05-21.034133
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_site_distrib.png


; 2025-05-21.034133
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites_per_peak.tab


; 2025-05-21.034133
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites_per_peak.png


; 2025-05-21.034133
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab


; 2025-05-21.034133
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_site_distrib.tab


; 2025-05-21.034134
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_site_distrib.png


; 2025-05-21.034134
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites_per_peak.tab


; 2025-05-21.034134
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites_per_peak.png


; 2025-05-21.034134
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_sites.tab


; 2025-05-21.034134
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_site_distrib.tab


; 2025-05-21.034134
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_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_8nt_mkv2_m1' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_site_distrib.png


; 2025-05-21.034134
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_sites_per_peak.tab


; 2025-05-21.034135
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_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_8nt_mkv2_m1' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_sites_per_peak.png


; 2025-05-21.034135
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_sites.tab


; 2025-05-21.034135
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_site_distrib.tab


; 2025-05-21.034135
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_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_8nt_mkv2_m2' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_site_distrib.png


; 2025-05-21.034135
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_sites_per_peak.tab


; 2025-05-21.034135
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_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_8nt_mkv2_m2' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_sites_per_peak.png


; 2025-05-21.034135
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_sites.tab


; 2025-05-21.034136
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_site_distrib.tab


; 2025-05-21.034136
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_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_8nt_mkv2_m3' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_site_distrib.png


; 2025-05-21.034136
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_sites_per_peak.tab


; 2025-05-21.034136
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_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_8nt_mkv2_m3' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_sites_per_peak.png


; 2025-05-21.034136
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_sites.tab


; 2025-05-21.034137
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_site_distrib.tab


; 2025-05-21.034137
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_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_8nt_mkv2_m4' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_site_distrib.png


; 2025-05-21.034137
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_sites_per_peak.tab


; 2025-05-21.034137
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_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_8nt_mkv2_m4' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_sites_per_peak.png


; 2025-05-21.034137
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_sites.tab


; 2025-05-21.034137
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_site_distrib.tab


; 2025-05-21.034137
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_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_8nt_mkv2_m5' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_site_distrib.png


; 2025-05-21.034138
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_sites_per_peak.tab


; 2025-05-21.034138
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_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_8nt_mkv2_m5' -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_sites_per_peak.png


; 2025-05-21.034138
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab


; 2025-05-21.034138
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab


; 2025-05-21.034138
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.png


; 2025-05-21.034138
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab


; 2025-05-21.034138
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.png


; 2025-05-21.034139
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab


; 2025-05-21.034139
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab


; 2025-05-21.034139
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.png


; 2025-05-21.034139
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab


; 2025-05-21.034139
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.png


; 2025-05-21.034139
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab


; 2025-05-21.034140
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.tab


; 2025-05-21.034140
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.png


; 2025-05-21.034140
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.tab


; 2025-05-21.034140
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.png


; 2025-05-21.034140
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab


; 2025-05-21.034141
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_site_distrib.tab


; 2025-05-21.034141
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_site_distrib.png


; 2025-05-21.034141
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_per_peak.tab


; 2025-05-21.034141
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites_per_peak.png


; 2025-05-21.034141
time -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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 200 -return sites -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab


; 2025-05-21.034141
grep -v '^;' $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_site_distrib.tab


; 2025-05-21.034142
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_site_distrib.png


; 2025-05-21.034142
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_per_peak.tab


; 2025-05-21.034142
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites_per_peak.png


; 2025-05-21.034142
cat $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_sites.tab $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_sites.tab > $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/sites/peak-motifs_all_motifs_seqcoord.tab


; 2025-05-21.034142
$RSAT/perl-scripts/text-to-html -font variable -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/reports/peak-motifs_timelog.txt -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/reports/peak-motifs_timelog.html

; peak-motifs  -v 1 -title MEyellowgreen -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifspeak_seq -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -offset 200 -motif_db footprintDB-plants tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2
; 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                	200
;	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         	8
;	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        	5
; Input files
;	motif_db_footprintDB-plants	/var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
;	test_seq              	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifspeak_seq
; Directories
;	output                        	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/
;	oligos_6nt_mkv2_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m1/
;	oligos_6nt_mkv2_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m2/
;	oligos_6nt_mkv2_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/
;	oligos_7nt_mkv2_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m1/
;	oligos_7nt_mkv2_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_7nt_mkv2_m2/
;	oligos_8nt_mkv2_m1            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/
;	oligos_8nt_mkv2_m2            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m2/
;	oligos_8nt_mkv2_m3            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m3/
;	oligos_8nt_mkv2_m4            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/
;	oligos_8nt_mkv2_m5            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/
;	dyads_m1                      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/
;	dyads_m2                      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/
;	dyads_m3                      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m3/
;	dyads_m4                      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m4/
;	dyads_m5                      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/
; Output files
;	1nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab
;	2nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab
;	archive                       	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifs_archive.zip
;	dyads                         	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_2pssm                   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
;	dyads_m1_logo                 	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_logo.png
;	dyads_m1_logo_rc              	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_logo_rc.png
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;	positions_7nt_pssm_logo3      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3.png
;	positions_7nt_pssm_logo4      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m4.png
;	positions_7nt_pssm_logo5      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m5.png
;	positions_7nt_pssm_logo_rc1   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m1_rc.png
;	positions_7nt_pssm_logo_rc2   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m5_rc.png
;	positions_7nt_pssm_sig        	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf
;	positions_8nt                 	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab
;	positions_8nt_2pssm           	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_log.txt
;	positions_8nt_asmb            	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm.asmb
;	positions_8nt_pssm_counts     	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices.txt
;	positions_8nt_pssm_logo1      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m1.png
;	positions_8nt_pssm_logo2      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m2.png
;	positions_8nt_pssm_logo3      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m3.png
;	positions_8nt_pssm_logo4      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m4.png
;	positions_8nt_pssm_logo5      	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m5.png
;	positions_8nt_pssm_logo_rc1   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m1_rc.png
;	positions_8nt_pssm_logo_rc2   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m2_rc.png
;	positions_8nt_pssm_logo_rc3   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m3_rc.png
;	positions_8nt_pssm_logo_rc4   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m4_rc.png
;	positions_8nt_pssm_logo_rc5   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m5_rc.png
;	positions_8nt_pssm_sig        	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_sig_matrices.tf
;	positions_8nt_pssm_tf         	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices.tf
;	small_summary                 	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifs_small_summary.html
;	small_summary_txt             	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/reports/peak-motifs_small_summary.txt
;	synthesis                     	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifs_synthesis.html
;	test_converted                	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test.fasta
;	test_purged                   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta
;	test_seqlen                   	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_seqlen.tab
;	test_seqlen_distrib           	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/data/sequences/peak-motifs_test_seqlen_distrib.png
;	timelog                       	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/reports/peak-motifs_timelog.txt
;	timelog_html                  	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/reports/peak-motifs_timelog.html
;	timetable                     	/var/www/html/rsat/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/reports/peak-motifs_timetable.txt

; 2025-05-21.034142
(cd $RSAT/public_html/tmp/www-data/2025/05/21 ;  zip -ryq peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifs_archive.zip peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2 -x peak-motifs_archive.zip)

