; 2026-01-22.160303
peak-motifs  -v 1 -title phoP -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifscontrol_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc



; 2026-01-22.160303
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/images_html


; 2026-01-22.160303
$RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifspeak_seq -from fasta -to fasta -mask non-dna | $RSAT/perl-scripts/sub-sequence -origin center -from -500 -to 499 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta


; 2026-01-22.160304
$RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -ml 40 -mis 3 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta


; 2026-01-22.160304
$RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_seqlen_distrib.tab


; 2026-01-22.160304
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; phoP' -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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_seqlen_distrib.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_seqlen_distrib.png


; 2026-01-22.160304
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -l 1 -1str -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab


; 2026-01-22.160304
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png


; 2026-01-22.160305
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -l 2 -1str -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab


; 2026-01-22.160305
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png


; 2026-01-22.160305
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 1 -ci 20 -img_format png -title 'phoP' -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab


; 2026-01-22.160307
grep -v ";" $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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; phoP' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png


; 2026-01-22.160307
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title 'phoP' -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab


; 2026-01-22.160310
grep -v ";" $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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; phoP' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png


; 2026-01-22.160310
$RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifscontrol_seq -from fasta -to fasta -mask non-dna | $RSAT/perl-scripts/sub-sequence -origin center -from -500 -to 499 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000.fasta


; 2026-01-22.160311
$RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000.fasta -ml 40 -mis 3 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta


; 2026-01-22.160311
$RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_seqlen_distrib.tab


; 2026-01-22.160311
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; phoP' -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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_seqlen_distrib.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_seqlen_distrib.png


; 2026-01-22.160311
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab_time.txt $RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta -l 1 -1str -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab


; 2026-01-22.160311
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_heatmap-1str-ovlp_1nt.png


; 2026-01-22.160312
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab_time.txt $RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta -l 2 -1str -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab


; 2026-01-22.160312
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_heatmap-1str-ovlp_2nt.png


; 2026-01-22.160312
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 1 -ci 20 -img_format png -title 'phoP' -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.tab


; 2026-01-22.160313
grep -v ";" $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_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; ctrl sequence; phoP' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.png


; 2026-01-22.160313
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.tab_time.txt $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort  -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title 'phoP' -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.tab


; 2026-01-22.160316
grep -v ";" $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_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; ctrl sequence; phoP' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.png


; 2026-01-22.160316
$RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 6 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_6nt-2str-noov.tab


; 2026-01-22.160316
$RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 7 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_7nt-2str-noov.tab


; 2026-01-22.160317
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_test_vs_ctrl.tab_time.txt $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -expfreq $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_6nt-2str-noov.tab -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_test_vs_ctrl.tab


; 2026-01-22.160317
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_test_vs_ctrl_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_test_vs_ctrl.tab -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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_test_vs_ctrl -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_test_vs_ctrl_pssm


; 2026-01-22.160325
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl.tab_time.txt $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 7 -expfreq $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos_bg_from_ctrl_7nt-2str-noov.tab -pseudo 0.01 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl.tab


; 2026-01-22.160326
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl_pssm_time.txt $RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl.tab -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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_test_vs_ctrl -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl_pssm


; 2026-01-22.160333
rm -f $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_6nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_6nt_test_vs_ctrl_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/oligos_7nt_test_vs_ctrl/peak-motifs_oligos-2str-noov_7nt_test_vs_ctrl_pssm_count_matrices.tf >> $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/peak-motifs_motifs_discovered.tf


; 2026-01-22.160333
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1.tab


; 2026-01-22.160333
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2.tab


; 2026-01-22.160333
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3.tab


; 2026-01-22.160334
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4.tab


; 2026-01-22.160334
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5.tab


; 2026-01-22.160334
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1.tab


; 2026-01-22.160334
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2.tab


; 2026-01-22.160334
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3.tab


; 2026-01-22.160334
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4.tab


; 2026-01-22.160334
$RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5.tab


; 2026-01-22.160335
$RSAT/perl-scripts/compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab; $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/peak-motifs_motifs_disco_compa.html


; 2026-01-22.160338
$RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml


; 2026-01-22.160338
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_sites.tab


; 2026-01-22.160339
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_site_distrib.tab


; 2026-01-22.160339
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_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_test_vs_ctrl_m1' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_site_distrib.png


; 2026-01-22.160339
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_sites_per_peak.tab


; 2026-01-22.160339
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_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_test_vs_ctrl_m1' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_sites_per_peak.png


; 2026-01-22.160339
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_sites.tab


; 2026-01-22.160340
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_site_distrib.tab


; 2026-01-22.160340
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_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_test_vs_ctrl_m2' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_site_distrib.png


; 2026-01-22.160340
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_sites_per_peak.tab


; 2026-01-22.160340
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_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_test_vs_ctrl_m2' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_sites_per_peak.png


; 2026-01-22.160340
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_sites.tab


; 2026-01-22.160341
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_site_distrib.tab


; 2026-01-22.160341
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_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_test_vs_ctrl_m3' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_site_distrib.png


; 2026-01-22.160341
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_sites_per_peak.tab


; 2026-01-22.160341
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_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_test_vs_ctrl_m3' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_sites_per_peak.png


; 2026-01-22.160341
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_sites.tab


; 2026-01-22.160342
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_site_distrib.tab


; 2026-01-22.160342
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_test_vs_ctrl_m4' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_site_distrib.png


; 2026-01-22.160342
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_sites_per_peak.tab


; 2026-01-22.160342
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_test_vs_ctrl_m4' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_sites_per_peak.png


; 2026-01-22.160342
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_sites.tab


; 2026-01-22.160343
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_site_distrib.tab


; 2026-01-22.160343
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_6nt_test_vs_ctrl_m5' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_site_distrib.png


; 2026-01-22.160343
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_sites_per_peak.tab


; 2026-01-22.160343
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_6nt_test_vs_ctrl_m5' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_sites_per_peak.png


; 2026-01-22.160343
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_sites.tab


; 2026-01-22.160344
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_site_distrib.tab


; 2026-01-22.160344
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_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_test_vs_ctrl_m1' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_site_distrib.png


; 2026-01-22.160344
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_sites_per_peak.tab


; 2026-01-22.160344
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_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_test_vs_ctrl_m1' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_sites_per_peak.png


; 2026-01-22.160344
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_sites.tab


; 2026-01-22.160344
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_site_distrib.tab


; 2026-01-22.160345
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_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_test_vs_ctrl_m2' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_site_distrib.png


; 2026-01-22.160345
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_sites_per_peak.tab


; 2026-01-22.160345
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_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_test_vs_ctrl_m2' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_sites_per_peak.png


; 2026-01-22.160345
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_sites.tab


; 2026-01-22.160345
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_site_distrib.tab


; 2026-01-22.160345
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_test_vs_ctrl_m3' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_site_distrib.png


; 2026-01-22.160346
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_sites_per_peak.tab


; 2026-01-22.160346
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_test_vs_ctrl_m3' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_sites_per_peak.png


; 2026-01-22.160346
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_sites.tab


; 2026-01-22.160346
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_site_distrib.tab


; 2026-01-22.160346
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_test_vs_ctrl_m4' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_site_distrib.png


; 2026-01-22.160347
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_sites_per_peak.tab


; 2026-01-22.160347
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_test_vs_ctrl_m4' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_sites_per_peak.png


; 2026-01-22.160347
time -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_sites.tab_time.txt $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt  -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score  -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_sites.tab


; 2026-01-22.160347
grep -v '^;' $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_site_distrib.tab


; 2026-01-22.160347
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 250 -ycol 4 -yleg1 'Number of sites' -xsize 600 -xcol 3 -xleg1 'Position relative to sequence center' -xgstep2 20 -vline '#666666' 0 -title1 'Predicted sites : oligos_7nt_test_vs_ctrl_m5' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_site_distrib.png


; 2026-01-22.160347
$RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_sites_per_peak.tab


; 2026-01-22.160348
$RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_sites_per_peak.tab -lines -xcol 1 -ycol 4  -xsize 500 -xcol 1 -xleg1 'Number of sites' -ysize 250 -ycol 4,6 -yleg1 'Number of peaks' -legend -xgstep1 5 -xgstep2 1 -title1 'Nb predicted sites : oligos_7nt_test_vs_ctrl_m5' -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_sites_per_peak.png


; 2026-01-22.160348
cat $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_sites.tab $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_sites.tab > $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/sites/peak-motifs_all_motifs_seqcoord.tab


; 2026-01-22.160348
$RSAT/perl-scripts/text-to-html -font variable -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/reports/peak-motifs_timelog.txt -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/reports/peak-motifs_timelog.html

; peak-motifs  -v 1 -title phoP -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifscontrol_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc
; Program version       	1.256
; Parameter values
;	seq_format            	fasta
;	img_format            	png
;	ref_motifs_format     	transfac
;	purge_match_length    	40
;	purge_mismatches      	3
;	origin                	center
;	offset                	0
;	profiles_ci           	20
;	profiles_max_graphs   	20
;	profiles_strand       	-1str
;	composition_oligo_lengths	1,2
;	profiles_noov         	-ovlp
;	strand                	-2str
;	disco_noov            	-noov
;	oligo_min_len         	6
;	oligo_max_len         	7
;	patterns_max_rank     	100
;	min_ratio             	1
;	min_zscore            	6
;	min_sig               	0
;	oligo_min_mkv         	auto
;	oligo_max_mkv         	auto
;	under_represented     	0
;	positions_max_graphs  	20
;	asmb_toppat           	100
;	max_asmb_width        	20
;	matrix_nmotifs        	5
; Input files
;	ctrl_seq              	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifscontrol_seq
;	test_seq              	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifspeak_seq
; Directories
;	output                        	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/
;	oligos_6nt_test_vs_ctrl_m1    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/
;	oligos_6nt_test_vs_ctrl_m2    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/
;	oligos_6nt_test_vs_ctrl_m3    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/
;	oligos_6nt_test_vs_ctrl_m4    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m4/
;	oligos_6nt_test_vs_ctrl_m5    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/
;	oligos_7nt_test_vs_ctrl_m1    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/
;	oligos_7nt_test_vs_ctrl_m2    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m2/
;	oligos_7nt_test_vs_ctrl_m3    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/
;	oligos_7nt_test_vs_ctrl_m4    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/
;	oligos_7nt_test_vs_ctrl_m5    	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/
; Output files
;	1nt_ctrl_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_1nt.tab
;	1nt_ctrl_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_heatmap-1str-ovlp_1nt.png
;	1nt_ctrl_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_inclusive-1str-ovlp_1nt.txt
;	1nt_ctrl_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_ctrl_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20.png
;	1nt_ctrl_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_ctrl_transitions          	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_1nt.tab
;	1nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab
;	2nt_ctrl_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_freq-1str-ovlp_2nt.tab
;	2nt_ctrl_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_heatmap-1str-ovlp_2nt.png
;	2nt_ctrl_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_inclusive-1str-ovlp_2nt.txt
;	2nt_ctrl_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_ctrl_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.png
;	2nt_ctrl_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_ctrl_transitions          	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_ctrl_transitions-1str-ovlp_2nt.tab
;	2nt_test_freq                 	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab
;	archive                       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifs_archive.zip
;	ctrl_converted                	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000.fasta
;	ctrl_purged                   	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta
;	ctrl_seqlen                   	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_ctrl_seqlen.tab
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;	test_purged                   	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta
;	test_seqlen                   	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_seqlen.tab
;	test_seqlen_distrib           	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/data/sequences/peak-motifs_test_seqlen_distrib.png
;	timelog                       	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/reports/peak-motifs_timelog.txt
;	timelog_html                  	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/reports/peak-motifs_timelog.html
;	timetable                     	/var/www/html/rsat/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/reports/peak-motifs_timetable.txt

; 2026-01-22.160348
(cd $RSAT/public_html/tmp/www-data/2026/01/22 ;  zip -ryq peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/peak-motifs_archive.zip peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc -x peak-motifs_archive.zip)

