; 2021-02-25.183603
peak-motifs  -i D6/regulonD6.rm.fna -ctrl Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna -motif_db footDB transfac $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -prefix peaks -outdir D6/regulonD6.rm.fna.peaks-rm -title D6/regulonD6.rm.fna -markov 2 -origin end -disco oligos,dyads,positions,local_words -nmotifs 5 -minol 5 -maxol 7 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_db,synthesis,small_summary,clean_seq



; 2021-02-25.183603
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  D6/regulonD6.rm.fna.peaks-rm/images_html


; 2021-02-25.183604
$RSAT/perl-scripts/convert-seq -i D6/regulonD6.rm.fna -from fasta -to fasta -mask non-dna -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test.fasta


; 2021-02-25.183604
$RSAT/perl-scripts/purge-sequence -dna -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -ml 40 -mis 3 -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta


; 2021-02-25.183605
$RSAT/perl-scripts/sequence-lengths -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen.tab -ci 20 -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.tab


; 2021-02-25.183606
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; D6/regulonD6.rm.fna' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.tab -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.png


; 2021-02-25.183606
time ($RSAT/bin/count-words -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -l 1 -1str > D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab_time.txt


; 2021-02-25.183606
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_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 D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png


; 2021-02-25.183607
time ($RSAT/bin/count-words -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta -l 2 -1str > D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab_time.txt


; 2021-02-25.183607
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_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 D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png


; 2021-02-25.183608
time ($RSAT/perl-scripts/position-analysis -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_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 'D6/regulonD6.rm.fna' -origin end -offset 0 -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab_time.txt


; 2021-02-25.183612
grep -v ";" D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_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; D6/regulonD6.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png


; 2021-02-25.183613
time ($RSAT/perl-scripts/position-analysis -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_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 'D6/regulonD6.rm.fna' -origin end -offset 0 -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab_time.txt


; 2021-02-25.183620
grep -v ";" D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_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; D6/regulonD6.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png


; 2021-02-25.183621
$RSAT/perl-scripts/convert-seq -i Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna -from fasta -to fasta -mask non-dna -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta


; 2021-02-25.183629
$RSAT/perl-scripts/purge-sequence -dna -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta -ml 40 -mis 3 -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta


; 2021-02-25.185721
$RSAT/perl-scripts/sequence-lengths -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab -ci 20 -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab


; 2021-02-25.185724
$RSAT/perl-scripts/XYgraph -lines -pointsize 0 -format png -title 'Peak lengths; D6/regulonD6.rm.fna' -xsize 700 -xcol 3 -xleg1 'Peak length' -ysize 250 -ycol 4 -yleg1 'Number of peaks' -xmin 0 -ymin 0 -xgstep2 20 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab -o D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.png


; 2021-02-25.185725
time ($RSAT/bin/count-words -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -l 1 -1str > D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab_time.txt


; 2021-02-25.185726
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_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 D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png


; 2021-02-25.185726
time ($RSAT/bin/count-words -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -l 2 -1str > D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab_time.txt


; 2021-02-25.185728
$RSAT/perl-scripts/convert-background-model -from oligos -to inclusive  -i D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt; $RSAT/perl-scripts/convert-background-model -from oligos -to transitions  -i D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_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 D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png


; 2021-02-25.185729
time ($RSAT/perl-scripts/position-analysis -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_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 'D6/regulonD6.rm.fna' -origin end -offset 0 -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab_time.txt


; 2021-02-25.190604
grep -v ";" D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_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; D6/regulonD6.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png


; 2021-02-25.190604
time ($RSAT/perl-scripts/position-analysis -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_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 'D6/regulonD6.rm.fna' -origin end -offset 0 -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab_time.txt


; 2021-02-25.191559
grep -v ";" D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_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; D6/regulonD6.rm.fna' -xleg1 'Position' -xsize 700 -yleg1 'Occurrences' -ysize 250  -ymin 0 -o D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png


; 2021-02-25.191600
$RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 5 -o D6/regulonD6.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_5nt-2str-noov.tab


; 2021-02-25.191608
$RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 6 -o D6/regulonD6.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab


; 2021-02-25.191618
$RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -format fasta -return occ,freq -2str -noov -seqtype dna -l 7 -o D6/regulonD6.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab


; 2021-02-25.191629
$RSAT/perl-scripts/dyad-analysis -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta -quick -format fasta -return occ,freq -2str -noov -seqtype dna -l 3 -sp 0-20  -o D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab


; 2021-02-25.191822
time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_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 5 -expfreq D6/regulonD6.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_5nt-2str-noov.tab -pseudo 0.01 -o D6/regulonD6.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab_time.txt


; 2021-02-25.191822
time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_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 -expfreq D6/regulonD6.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab -pseudo 0.01 -o D6/regulonD6.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab_time.txt


; 2021-02-25.191824
time ($RSAT/perl-scripts/oligo-analysis -v 1 -quick -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_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 -expfreq D6/regulonD6.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab -pseudo 0.01 -o D6/regulonD6.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab_time.txt


; 2021-02-25.191829
cat D6/regulonD6.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab D6/regulonD6.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab D6/regulonD6.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab> D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab


; 2021-02-25.191829
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -pl D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2.tab -bgfile D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_5-7nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm) >& D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_time.txt


; 2021-02-25.191842
time ($RSAT/perl-scripts/dyad-analysis -v 1 -i D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_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  -expfreq D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab -pseudo 0.01 | perl -pe 's/n\{0\}//g' >D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab_time.txt


; 2021-02-25.191902
time ($RSAT/perl-scripts/matrix-from-patterns -v 1  -sites -seq D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test.fasta -pl D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix dyads_test_vs_ctrl -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm) >& D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_time.txt


; 2021-02-25.191915
rm -f D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf; cat D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf >> D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf; cat D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf >> D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf


; 2021-02-25.191915
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tab


; 2021-02-25.191915
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2.tab


; 2021-02-25.191916
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3.tab


; 2021-02-25.191917
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4.tab


; 2021-02-25.191917
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5.tab


; 2021-02-25.191917
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tab


; 2021-02-25.191918
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tab


; 2021-02-25.191918
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tab


; 2021-02-25.191919
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tab


; 2021-02-25.191919
$RSAT/perl-scripts/convert-matrix -v 0 -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tf -from transfac -to tab -return counts -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tab


; 2021-02-25.191919
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/peaks_oligos_5-7nt_m1_vs_db_footDB


; 2021-02-25.191926
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/peaks_oligos_5-7nt_m2_vs_db_footDB


; 2021-02-25.191933
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/peaks_oligos_5-7nt_m3_vs_db_footDB


; 2021-02-25.191940
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/peaks_oligos_5-7nt_m4_vs_db_footDB


; 2021-02-25.191946
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/peaks_oligos_5-7nt_m5_vs_db_footDB


; 2021-02-25.191953
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footDB


; 2021-02-25.191959
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footDB


; 2021-02-25.192005
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footDB


; 2021-02-25.192013
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_db_footDB


; 2021-02-25.192020
$RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_db_footDB


; 2021-02-25.192027
time ($RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.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 D6/regulonD6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab) >& D6/regulonD6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab_time.txt


; 2021-02-25.192040
$RSAT/perl-scripts/convert-graph -i D6/regulonD6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o D6/regulonD6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.gml

; peak-motifs  -i D6/regulonD6.rm.fna -ctrl Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna -motif_db footDB transfac $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -prefix peaks -outdir D6/regulonD6.rm.fna.peaks-rm -title D6/regulonD6.rm.fna -markov 2 -origin end -disco oligos,dyads,positions,local_words -nmotifs 5 -minol 5 -maxol 7 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_db,synthesis,small_summary,clean_seq
; Program version       	1.256
; Parameter values
;	seq_format            	fasta
;	img_format            	png
;	ref_motifs_format     	transfac
;	purge_match_length    	40
;	purge_mismatches      	3
;	origin                	end
;	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         	5
;	oligo_max_len         	7
;	patterns_max_rank     	100
;	min_ratio             	1
;	min_zscore            	6
;	min_sig               	0
;	oligo_min_mkv         	2
;	oligo_max_mkv         	2
;	under_represented     	0
;	positions_max_graphs  	20
;	asmb_toppat           	100
;	max_asmb_width        	20
;	matrix_nmotifs        	5
; Input files
;	ctrl_seq              	Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna
;	motif_db_footDB       	/var/www/html/rsat/_footprintDB/footprintDB.transfac.plants.motif.tf
;	test_seq              	D6/regulonD6.rm.fna
; Directories
;	output                        	D6/regulonD6.rm.fna.peaks-rm/
;	oligos_5-7nt_m1               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/
;	oligos_5-7nt_m2               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/
;	oligos_5-7nt_m3               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/
;	oligos_5-7nt_m4               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/
;	oligos_5-7nt_m5               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/
;	dyads_test_vs_ctrl_m1         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/
;	dyads_test_vs_ctrl_m2         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/
;	dyads_test_vs_ctrl_m3         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/
;	dyads_test_vs_ctrl_m4         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/
;	dyads_test_vs_ctrl_m5         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/
; Output files
;	1nt_ctrl_freq                 	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab
;	1nt_ctrl_heatmap              	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png
;	1nt_ctrl_inclusive            	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt
;	1nt_ctrl_profiles             	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_ctrl_profiles_graph       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png
;	1nt_ctrl_profiles_index       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_ctrl_transitions          	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab
;	1nt_test_freq                 	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab
;	2nt_ctrl_freq                 	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab
;	2nt_ctrl_heatmap              	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png
;	2nt_ctrl_inclusive            	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt
;	2nt_ctrl_profiles             	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_ctrl_profiles_graph       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png
;	2nt_ctrl_profiles_index       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_ctrl_transitions          	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab
;	2nt_test_freq                 	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab
;	archive                       	D6/regulonD6.rm.fna.peaks-rm/peaks_archive.zip
;	ctrl_converted                	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta
;	ctrl_purged                   	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta
;	ctrl_seqlen                   	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab
;	ctrl_seqlen_distrib           	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab
;	ctrl_seqlen_distrib_graph     	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.png
;	dyads_test_vs_ctrl            	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_test_vs_ctrl_2pssm      	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt
;	dyads_test_vs_ctrl_asmb       	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
;	dyads_test_vs_ctrl_bg_file    	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_test_vs_ctrl_m1_logo    	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo.png
;	dyads_test_vs_ctrl_m1_logo_rc 	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo_rc.png
;	dyads_test_vs_ctrl_m1_pssm_enrichment	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m1_pssm_enrichment_png	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m1_pssm_site_distrib	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_site_distrib.tab
;	dyads_test_vs_ctrl_m1_pssm_site_distrib_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_site_distrib.png
;	dyads_test_vs_ctrl_m1_pssm_sites	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites.tab
;	dyads_test_vs_ctrl_m1_pssm_sites_per_peak	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites_per_peak.tab
;	dyads_test_vs_ctrl_m1_pssm_sites_per_peak_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites_per_peak.png
;	dyads_test_vs_ctrl_m1_tab     	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tab
;	dyads_test_vs_ctrl_m1_tf      	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf
;	dyads_test_vs_ctrl_m1_vs_db_footDB	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footDB.tab
;	dyads_test_vs_ctrl_m1_vs_db_footDB_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footDB.html
;	dyads_test_vs_ctrl_m1_vs_ref  	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_ref.tab
;	dyads_test_vs_ctrl_m1_vs_ref_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_ref.html
;	dyads_test_vs_ctrl_m2_logo    	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo.png
;	dyads_test_vs_ctrl_m2_logo_rc 	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo_rc.png
;	dyads_test_vs_ctrl_m2_pssm_enrichment	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m2_pssm_enrichment_png	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m2_pssm_site_distrib	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_site_distrib.tab
;	dyads_test_vs_ctrl_m2_pssm_site_distrib_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_site_distrib.png
;	dyads_test_vs_ctrl_m2_pssm_sites	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites.tab
;	dyads_test_vs_ctrl_m2_pssm_sites_per_peak	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites_per_peak.tab
;	dyads_test_vs_ctrl_m2_pssm_sites_per_peak_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites_per_peak.png
;	dyads_test_vs_ctrl_m2_tab     	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tab
;	dyads_test_vs_ctrl_m2_tf      	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf
;	dyads_test_vs_ctrl_m2_vs_db_footDB	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footDB.tab
;	dyads_test_vs_ctrl_m2_vs_db_footDB_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footDB.html
;	dyads_test_vs_ctrl_m2_vs_ref  	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_ref.tab
;	dyads_test_vs_ctrl_m2_vs_ref_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_ref.html
;	dyads_test_vs_ctrl_m3_logo    	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_logo.png
;	dyads_test_vs_ctrl_m3_logo_rc 	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_logo_rc.png
;	dyads_test_vs_ctrl_m3_pssm_enrichment	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m3_pssm_enrichment_png	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m3_pssm_site_distrib	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_site_distrib.tab
;	dyads_test_vs_ctrl_m3_pssm_site_distrib_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_site_distrib.png
;	dyads_test_vs_ctrl_m3_pssm_sites	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites.tab
;	dyads_test_vs_ctrl_m3_pssm_sites_per_peak	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites_per_peak.tab
;	dyads_test_vs_ctrl_m3_pssm_sites_per_peak_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites_per_peak.png
;	dyads_test_vs_ctrl_m3_tab     	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tab
;	dyads_test_vs_ctrl_m3_tf      	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3.tf
;	dyads_test_vs_ctrl_m3_vs_db_footDB	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footDB.tab
;	dyads_test_vs_ctrl_m3_vs_db_footDB_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_db_footDB.html
;	dyads_test_vs_ctrl_m3_vs_ref  	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_ref.tab
;	dyads_test_vs_ctrl_m3_vs_ref_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_vs_ref.html
;	dyads_test_vs_ctrl_m4_logo    	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_logo.png
;	dyads_test_vs_ctrl_m4_logo_rc 	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_logo_rc.png
;	dyads_test_vs_ctrl_m4_pssm_enrichment	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m4_pssm_enrichment_png	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m4_pssm_site_distrib	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_site_distrib.tab
;	dyads_test_vs_ctrl_m4_pssm_site_distrib_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_site_distrib.png
;	dyads_test_vs_ctrl_m4_pssm_sites	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_sites.tab
;	dyads_test_vs_ctrl_m4_pssm_sites_per_peak	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_sites_per_peak.tab
;	dyads_test_vs_ctrl_m4_pssm_sites_per_peak_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_sites_per_peak.png
;	dyads_test_vs_ctrl_m4_tab     	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tab
;	dyads_test_vs_ctrl_m4_tf      	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf
;	dyads_test_vs_ctrl_m4_vs_db_footDB	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_db_footDB.tab
;	dyads_test_vs_ctrl_m4_vs_db_footDB_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_db_footDB.html
;	dyads_test_vs_ctrl_m4_vs_ref  	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_ref.tab
;	dyads_test_vs_ctrl_m4_vs_ref_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4_vs_ref.html
;	dyads_test_vs_ctrl_m5_logo    	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_logo.png
;	dyads_test_vs_ctrl_m5_logo_rc 	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_logo_rc.png
;	dyads_test_vs_ctrl_m5_pssm_enrichment	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m5_pssm_enrichment_png	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m5_pssm_site_distrib	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_site_distrib.tab
;	dyads_test_vs_ctrl_m5_pssm_site_distrib_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_site_distrib.png
;	dyads_test_vs_ctrl_m5_pssm_sites	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_sites.tab
;	dyads_test_vs_ctrl_m5_pssm_sites_per_peak	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_sites_per_peak.tab
;	dyads_test_vs_ctrl_m5_pssm_sites_per_peak_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_sites_per_peak.png
;	dyads_test_vs_ctrl_m5_tab     	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tab
;	dyads_test_vs_ctrl_m5_tf      	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5.tf
;	dyads_test_vs_ctrl_m5_vs_db_footDB	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_db_footDB.tab
;	dyads_test_vs_ctrl_m5_vs_db_footDB_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_db_footDB.html
;	dyads_test_vs_ctrl_m5_vs_ref  	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_ref.tab
;	dyads_test_vs_ctrl_m5_vs_ref_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/peaks_dyads_test_vs_ctrl_m5_vs_ref.html
;	dyads_test_vs_ctrl_pssm_counts	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.txt
;	dyads_test_vs_ctrl_pssm_logo1 	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m1.png
;	dyads_test_vs_ctrl_pssm_logo2 	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m2.png
;	dyads_test_vs_ctrl_pssm_logo3 	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m3.png
;	dyads_test_vs_ctrl_pssm_logo4 	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m4.png
;	dyads_test_vs_ctrl_pssm_logo5 	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m5.png
;	dyads_test_vs_ctrl_pssm_logo_rc1	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m1_rc.png
;	dyads_test_vs_ctrl_pssm_logo_rc2	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m2_rc.png
;	dyads_test_vs_ctrl_pssm_logo_rc3	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m3_rc.png
;	dyads_test_vs_ctrl_pssm_logo_rc4	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m4_rc.png
;	dyads_test_vs_ctrl_pssm_logo_rc5	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices_logo_m5_rc.png
;	dyads_test_vs_ctrl_pssm_sig   	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_sig_matrices.tf
;	dyads_test_vs_ctrl_pssm_tf    	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf
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;	oligos_5-7nt_pssm_logo_rc3    	D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m3_rc.png
;	oligos_5-7nt_pssm_logo_rc4    	D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m4_rc.png
;	oligos_5-7nt_pssm_logo_rc5    	D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices_logo_m5_rc.png
;	oligos_5-7nt_pssm_sig         	D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_sig_matrices.tf
;	oligos_5-7nt_pssm_tf          	D6/regulonD6.rm.fna.peaks-rm/results/oligos_5-7nt/peaks_oligos-2str-noov_5-7nt_mvk2_2_pssm_count_matrices.tf
;	oligos_5nt_test_vs_ctrl       	D6/regulonD6.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos-2str-noov_5nt_test_vs_ctrl.tab
;	oligos_5nt_test_vs_ctrl_bg_file	D6/regulonD6.rm.fna.peaks-rm/results/oligos_5nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_5nt-2str-noov.tab
;	oligos_6nt_test_vs_ctrl       	D6/regulonD6.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos-2str-noov_6nt_test_vs_ctrl.tab
;	oligos_6nt_test_vs_ctrl_bg_file	D6/regulonD6.rm.fna.peaks-rm/results/oligos_6nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_6nt-2str-noov.tab
;	oligos_7nt_test_vs_ctrl       	D6/regulonD6.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos-2str-noov_7nt_test_vs_ctrl.tab
;	oligos_7nt_test_vs_ctrl_bg_file	D6/regulonD6.rm.fna.peaks-rm/results/oligos_7nt_test_vs_ctrl/peaks_oligos_bg_from_ctrl_7nt-2str-noov.tab
;	small_summary                 	D6/regulonD6.rm.fna.peaks-rm/peaks_small_summary.html
;	small_summary_txt             	D6/regulonD6.rm.fna.peaks-rm/reports/peaks_small_summary.txt
;	synthesis                     	D6/regulonD6.rm.fna.peaks-rm/peaks_synthesis.html
;	test_converted                	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test.fasta
;	test_purged                   	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta
;	test_seqlen                   	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen.tab
;	test_seqlen_distrib           	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.tab
;	test_seqlen_distrib_graph     	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_seqlen_distrib.png
;	timelog                       	D6/regulonD6.rm.fna.peaks-rm/reports/peaks_timelog.txt
;	timelog_html                  	D6/regulonD6.rm.fna.peaks-rm/reports/peaks_timelog.html
;	timetable                     	D6/regulonD6.rm.fna.peaks-rm/reports/peaks_timetable.txt

; 2021-02-25.192156
rm -f D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_test_purged_ml40_mis3.fasta


; 2021-02-25.192156
rm -f D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta


; 2021-02-25.192156
rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg  D6/regulonD6.rm.fna.peaks-rm/images_html

; peak-motifs  -i D6/regulonD6.rm.fna -ctrl Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna -motif_db footDB transfac $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -prefix peaks -outdir D6/regulonD6.rm.fna.peaks-rm -title D6/regulonD6.rm.fna -markov 2 -origin end -disco oligos,dyads,positions,local_words -nmotifs 5 -minol 5 -maxol 7 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_db,synthesis,small_summary,clean_seq
; Program version       	1.256
; Parameter values
;	seq_format            	fasta
;	img_format            	png
;	ref_motifs_format     	transfac
;	purge_match_length    	40
;	purge_mismatches      	3
;	origin                	end
;	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         	5
;	oligo_max_len         	7
;	patterns_max_rank     	100
;	min_ratio             	1
;	min_zscore            	6
;	min_sig               	0
;	oligo_min_mkv         	2
;	oligo_max_mkv         	2
;	under_represented     	0
;	positions_max_graphs  	20
;	asmb_toppat           	100
;	max_asmb_width        	20
;	matrix_nmotifs        	5
; Input files
;	ctrl_seq              	Brachypodium_distachyon.Brachypodium_distachyon_v3.0.46-upstream.rm.fna
;	motif_db_footDB       	/var/www/html/rsat/_footprintDB/footprintDB.transfac.plants.motif.tf
;	test_seq              	D6/regulonD6.rm.fna
; Directories
;	output                        	D6/regulonD6.rm.fna.peaks-rm/
;	oligos_5-7nt_m1               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m1/
;	oligos_5-7nt_m2               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m2/
;	oligos_5-7nt_m3               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m3/
;	oligos_5-7nt_m4               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m4/
;	oligos_5-7nt_m5               	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/oligos_5-7nt_m5/
;	dyads_test_vs_ctrl_m1         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/
;	dyads_test_vs_ctrl_m2         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/
;	dyads_test_vs_ctrl_m3         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/
;	dyads_test_vs_ctrl_m4         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m4/
;	dyads_test_vs_ctrl_m5         	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m5/
; Output files
;	1nt_ctrl_freq                 	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_1nt.tab
;	1nt_ctrl_heatmap              	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_1nt.png
;	1nt_ctrl_inclusive            	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_1nt.txt
;	1nt_ctrl_profiles             	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_ctrl_profiles_graph       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.png
;	1nt_ctrl_profiles_index       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_ctrl_transitions          	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_1nt.tab
;	1nt_test_freq                 	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_1nt.tab
;	1nt_test_heatmap              	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_1nt.png
;	1nt_test_inclusive            	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_1nt.txt
;	1nt_test_profiles             	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.tab
;	1nt_test_profiles_graph       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20.png
;	1nt_test_profiles_index       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_1nt_ci20_graph_index.html
;	1nt_test_transitions          	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_1nt.tab
;	2nt_ctrl_freq                 	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_freq-1str-ovlp_2nt.tab
;	2nt_ctrl_heatmap              	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_heatmap-1str-ovlp_2nt.png
;	2nt_ctrl_inclusive            	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_inclusive-1str-ovlp_2nt.txt
;	2nt_ctrl_profiles             	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_ctrl_profiles_graph       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20.png
;	2nt_ctrl_profiles_index       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_ctrl_transitions          	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_ctrl_transitions-1str-ovlp_2nt.tab
;	2nt_test_freq                 	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_freq-1str-ovlp_2nt.tab
;	2nt_test_heatmap              	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_heatmap-1str-ovlp_2nt.png
;	2nt_test_inclusive            	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_inclusive-1str-ovlp_2nt.txt
;	2nt_test_profiles             	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.tab
;	2nt_test_profiles_graph       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20.png
;	2nt_test_profiles_index       	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_profiles-1str-ovlp_2nt_ci20_graph_index.html
;	2nt_test_transitions          	D6/regulonD6.rm.fna.peaks-rm/results/composition/peaks_test_transitions-1str-ovlp_2nt.tab
;	archive                       	D6/regulonD6.rm.fna.peaks-rm/peaks_archive.zip
;	ctrl_converted                	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl.fasta
;	ctrl_purged                   	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta
;	ctrl_seqlen                   	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen.tab
;	ctrl_seqlen_distrib           	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.tab
;	ctrl_seqlen_distrib_graph     	D6/regulonD6.rm.fna.peaks-rm/data/sequences/peaks_ctrl_seqlen_distrib.png
;	dyads_test_vs_ctrl            	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_test_vs_ctrl_2pssm      	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt
;	dyads_test_vs_ctrl_asmb       	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb
;	dyads_test_vs_ctrl_bg_file    	D6/regulonD6.rm.fna.peaks-rm/results/dyads_test_vs_ctrl/peaks_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab
;	dyads_test_vs_ctrl_m1_logo    	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo.png
;	dyads_test_vs_ctrl_m1_logo_rc 	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_logo_rc.png
;	dyads_test_vs_ctrl_m1_pssm_enrichment	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m1_pssm_enrichment_png	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m1_pssm_site_distrib	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_site_distrib.tab
;	dyads_test_vs_ctrl_m1_pssm_site_distrib_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_site_distrib.png
;	dyads_test_vs_ctrl_m1_pssm_sites	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites.tab
;	dyads_test_vs_ctrl_m1_pssm_sites_per_peak	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites_per_peak.tab
;	dyads_test_vs_ctrl_m1_pssm_sites_per_peak_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_sites_per_peak.png
;	dyads_test_vs_ctrl_m1_tab     	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tab
;	dyads_test_vs_ctrl_m1_tf      	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1.tf
;	dyads_test_vs_ctrl_m1_vs_db_footDB	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footDB.tab
;	dyads_test_vs_ctrl_m1_vs_db_footDB_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_db_footDB.html
;	dyads_test_vs_ctrl_m1_vs_ref  	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_ref.tab
;	dyads_test_vs_ctrl_m1_vs_ref_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m1/peaks_dyads_test_vs_ctrl_m1_vs_ref.html
;	dyads_test_vs_ctrl_m2_logo    	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo.png
;	dyads_test_vs_ctrl_m2_logo_rc 	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_logo_rc.png
;	dyads_test_vs_ctrl_m2_pssm_enrichment	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m2_pssm_enrichment_png	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m2_pssm_site_distrib	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_site_distrib.tab
;	dyads_test_vs_ctrl_m2_pssm_site_distrib_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_site_distrib.png
;	dyads_test_vs_ctrl_m2_pssm_sites	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites.tab
;	dyads_test_vs_ctrl_m2_pssm_sites_per_peak	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites_per_peak.tab
;	dyads_test_vs_ctrl_m2_pssm_sites_per_peak_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_sites_per_peak.png
;	dyads_test_vs_ctrl_m2_tab     	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tab
;	dyads_test_vs_ctrl_m2_tf      	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2.tf
;	dyads_test_vs_ctrl_m2_vs_db_footDB	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footDB.tab
;	dyads_test_vs_ctrl_m2_vs_db_footDB_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_db_footDB.html
;	dyads_test_vs_ctrl_m2_vs_ref  	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_ref.tab
;	dyads_test_vs_ctrl_m2_vs_ref_html	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m2/peaks_dyads_test_vs_ctrl_m2_vs_ref.html
;	dyads_test_vs_ctrl_m3_logo    	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_logo.png
;	dyads_test_vs_ctrl_m3_logo_rc 	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_logo_rc.png
;	dyads_test_vs_ctrl_m3_pssm_enrichment	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_scan_mkv1_enrichment.tab
;	dyads_test_vs_ctrl_m3_pssm_enrichment_png	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_scan_mkv1_enrichment.png
;	dyads_test_vs_ctrl_m3_pssm_site_distrib	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_site_distrib.tab
;	dyads_test_vs_ctrl_m3_pssm_site_distrib_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_site_distrib.png
;	dyads_test_vs_ctrl_m3_pssm_sites	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites.tab
;	dyads_test_vs_ctrl_m3_pssm_sites_per_peak	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites_per_peak.tab
;	dyads_test_vs_ctrl_m3_pssm_sites_per_peak_graph	D6/regulonD6.rm.fna.peaks-rm/results/discovered_motifs/dyads_test_vs_ctrl_m3/peaks_dyads_test_vs_ctrl_m3_sites_per_peak.png
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; 2021-02-25.192156
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