; 2014-09-06.011250 peak-motifs -v 1 -title ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -motif_db regulonDB tf $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -motif_db footprintDB tf $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN ; 2014-09-06.011250 rsync -ruptl $RSAT/perl-scripts/lib/images/arrow*.gif $RSAT/perl-scripts/lib/images/UCSC_icon.jpg $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/images_html ; 2014-09-06.011250 $RSAT/perl-scripts/convert-seq -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta ; 2014-09-06.011250 $RSAT/perl-scripts/purge-sequence -dna -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -ml 30 -mis 0 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta ; 2014-09-06.011251 $RSAT/perl-scripts/sequence-lengths -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_seqlen.tab ; $RSAT/perl-scripts/classfreq -v 1 -col 2 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_seqlen.tab -ci 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_seqlen_distrib.tab ; 2014-09-06.011251 $RSAT/perl-scripts/XYgraph -lines -pointsize 0 -legend -format png -title 'Sequence lengths; ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps' -ysize 200 -ycol 4 -yleg1 'Number of peaks' -xsize 800 -xcol 3 -xleg1 'Peak length' -xmin 0 -ymin 0 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_seqlen_distrib.tab -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_seqlen_distrib.png ; 2014-09-06.011252 $RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -l 1 -1str > $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab ; 2014-09-06.011252 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -out_format png -col_width 50 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png ; 2014-09-06.011252 $RSAT/bin/count-words -v 1 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -l 2 -1str > $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab ; 2014-09-06.011252 $RSAT/perl-scripts/convert-background-model -from oligos -to inclusive -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; cut -f 1-5,7 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab | $RSAT/perl-scripts/draw-heatmap -min 0 -max 1 -out_format png -col_width 50 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png ; 2014-09-06.011253 $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.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 'ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps' -origin center -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab ; 2014-09-06.011255 grep -v ";" $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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 -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; ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300 -ymin 0 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png ; 2014-09-06.011255 $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.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 'ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps' -origin center -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab ; 2014-09-06.011300 grep -v ";" $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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 -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; ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps' -xleg1 'Position' -xsize 800 -yleg1 'Occurrences' -ysize 300 -ymin 0 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png ; 2014-09-06.011301 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 6 -markov 2 -pseudo 0.01 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.tab ; 2014-09-06.011302 $RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.tab -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_6nt_mkv2 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm ; 2014-09-06.011306 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 7 -markov 2 -pseudo 0.01 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.tab ; 2014-09-06.011307 $RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.tab -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_7nt_mkv2 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm ; 2014-09-06.011311 $RSAT/perl-scripts/oligo-analysis -v 1 -quick -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,rank -2str -noov -seqtype dna -l 8 -markov 2 -pseudo 0.01 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2.tab ; 2014-09-06.011314 $RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2.tab -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix oligos_8nt_mkv2 -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2_pssm ; 2014-09-06.011317 $RSAT/perl-scripts/dyad-analysis -v 1 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -quick -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,ratio,zscore,rank -2str -noov -seqtype dna -l 3 -sp 0-20 -bg monads -pseudo 0.01 | perl -pe 's/n\{0\}//g' >$RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab ; 2014-09-06.011326 $RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 0 -prefix dyads -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm ; 2014-09-06.011334 $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -format fasta -sort -return html,chi,sig,distrib,exp_occ,graphs,rank,index -max_graphs 100 -2str -noov -seqtype dna -l 6 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps' -origin center -max_graphs 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab ; 2014-09-06.011336 $RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix positions_6nt -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm ; 2014-09-06.011336 $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -format fasta -sort -return html,chi,sig,distrib,exp_occ,graphs,rank,index -max_graphs 100 -2str -noov -seqtype dna -l 7 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps' -origin center -max_graphs 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab ; 2014-09-06.011339 $RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix positions_7nt -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm ; 2014-09-06.011339 $RSAT/perl-scripts/position-analysis -v 1 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -format fasta -sort -return html,chi,sig,distrib,exp_occ,graphs,rank,index -max_graphs 100 -2str -noov -seqtype dna -l 8 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title 'ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps' -origin center -max_graphs 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab ; 2014-09-06.011342 $RSAT/perl-scripts/matrix-from-patterns -v 1 -seq $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -pl $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 5 -max_asmb_width 20 -subst 1 -prefix positions_8nt -flanks 2 -collect_method matrix-scan-quick -logo -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm ; 2014-09-06.011343 $RSAT/perl-scripts/compare-scores -v 1 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.tab -sc1 8 -suppress $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/ -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab -sc2 9 -suppress $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_6nt/ -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.tab -sc3 8 -suppress $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/ -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -sc4 9 -suppress $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/ -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2.tab -sc5 8 -suppress $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_8nt_mkv2/ -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab -sc6 9 -suppress $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/ -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab -sc7 8 -suppress $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/dyads/ -ic 1 -lc -null . -suppress peak-motifs_ -suppress '.tab' | $RSAT/perl-scripts/row-stats -after 1 -sort -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/merged_words/peak-motifs_merged_words.tab ; 2014-09-06.011343 $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/merged_words/peak-motifs_merged_words.tab -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/merged_words/peak-motifs_merged_words.html ; 2014-09-06.011343 $RSAT/perl-scripts/draw-heatmap -min 0 -max 10 -out_format png -col_width 40 -rownames -gradient fire -row_height 16 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/merged_words/peak-motifs_merged_words.tab -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/merged_words/peak-motifs_merged_words_heatmap.png ; 2014-09-06.011343 rm -f $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices.tf >> $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices.tf >> $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2_pssm_count_matrices.tf >> $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf; cat $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_count_matrices.tf >> $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf ; 2014-09-06.011343 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tab ; 2014-09-06.011344 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tab ; 2014-09-06.011344 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tab ; 2014-09-06.011344 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tab ; 2014-09-06.011345 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tab ; 2014-09-06.011345 $RSAT/perl-scripts/convert-matrix -v 0 -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -from transfac -to tab -return counts -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tab ; 2014-09-06.011345 $RSAT/perl-scripts/compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab; $RSAT/perl-scripts/text-to-html -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_disco_compa.html ; 2014-09-06.011348 $RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml ; 2014-09-06.011348 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_regulonDB ; 2014-09-06.011350 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_regulonDB ; 2014-09-06.011352 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_regulonDB ; 2014-09-06.011353 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_regulonDB ; 2014-09-06.011355 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_regulonDB ; 2014-09-06.011358 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_regulonDB ; 2014-09-06.011359 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB.tab ; 2014-09-06.011407 $RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB.gml ; 2014-09-06.011407 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB ; 2014-09-06.011454 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB ; 2014-09-06.011527 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_vs_db_footprintDB ; 2014-09-06.011601 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_footprintDB ; 2014-09-06.011646 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB ; 2014-09-06.011734 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB ; 2014-09-06.011812 $RSAT/perl-scripts/compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB.tab ; 2014-09-06.012136 $RSAT/perl-scripts/convert-graph -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB.tab -ewidth -ecolors fire -layout spring -from tab -to gml -scol 3 -tcol 4 -wcol 5 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB.gml ; 2014-09-06.012141 $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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 -return sites -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites.tab ; 2014-09-06.012142 grep -v '^;' $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_site_distrib.tab ; 2014-09-06.012142 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_6nt_mkv2' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_site_distrib.png ; 2014-09-06.012142 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites_per_peak.tab ; 2014-09-06.012142 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_6nt_mkv2' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites_per_peak.png ; 2014-09-06.012143 $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_scan_mkv1_enrichment.tab ; 2014-09-06.012144 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_scan_mkv1_enrichment.png ; 2014-09-06.012144 $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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 -return sites -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites.tab ; 2014-09-06.012145 grep -v '^;' $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_site_distrib.tab ; 2014-09-06.012145 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_7nt_mkv2' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_site_distrib.png ; 2014-09-06.012145 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites_per_peak.tab ; 2014-09-06.012145 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_7nt_mkv2' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites_per_peak.png ; 2014-09-06.012146 $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_scan_mkv1_enrichment.tab ; 2014-09-06.012147 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_scan_mkv1_enrichment.png ; 2014-09-06.012147 $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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 -return sites -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites.tab ; 2014-09-06.012148 grep -v '^;' $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_site_distrib.tab ; 2014-09-06.012148 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : oligos_8nt_mkv2' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_site_distrib.png ; 2014-09-06.012148 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites_per_peak.tab ; 2014-09-06.012148 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : oligos_8nt_mkv2' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites_per_peak.png ; 2014-09-06.012149 $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_scan_mkv1_enrichment.tab ; 2014-09-06.012150 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_scan_mkv1_enrichment.png ; 2014-09-06.012150 $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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 -return sites -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab ; 2014-09-06.012151 grep -v '^;' $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab ; 2014-09-06.012151 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : dyads_m1' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.png ; 2014-09-06.012151 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab ; 2014-09-06.012151 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : dyads_m1' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.png ; 2014-09-06.012152 $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.tab ; 2014-09-06.012155 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.png ; 2014-09-06.012155 $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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 -return sites -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab ; 2014-09-06.012156 grep -v '^;' $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab ; 2014-09-06.012156 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : dyads_m2' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.png ; 2014-09-06.012156 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab ; 2014-09-06.012157 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : dyads_m2' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.png ; 2014-09-06.012157 $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.tab ; 2014-09-06.012200 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.png ; 2014-09-06.012200 $RSAT/perl-scripts/matrix-scan -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/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 -return sites -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab ; 2014-09-06.012201 grep -v '^;' $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab | grep -v '^#' | awk '{print ($6+$5)/2}' | $RSAT/perl-scripts/classfreq -v 1 -ci 20 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.tab ; 2014-09-06.012201 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.tab -lines -xcol 3 -ycol 4 -ysize 200 -ycol 4 -yleg1 'Number of sites' -xsize 800 -xcol 3 -xleg1 'Sequence position relative to peak center' -title1 'Predicted sites : dyads_m3' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_site_distrib.png ; 2014-09-06.012201 $RSAT/perl-scripts/contingency-table -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab | $RSAT/perl-scripts/classfreq -v 1 -ci 1 -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.tab ; 2014-09-06.012202 $RSAT/perl-scripts/XYgraph -format png -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.tab -lines -xcol 1 -ycol 4 -ysize 200 -ycol 4,6 -yleg1 'Number of peaks' -legend -xsize 400 -xcol 1 -xleg1 'Number of sites' -xgstep1 5 -xgstep2 1 -title1 'Nb Predicted sites : dyads_m3' -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites_per_peak.png ; 2014-09-06.012202 $RSAT/perl-scripts/matrix-scan -v 1 -quick -seq_format fasta -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score -5 -bginput -markov 1 -return distrib -return occ_proba -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.tab ; 2014-09-06.012203 $RSAT/perl-scripts/XYgraph -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.tab -xcol 2 -xleg1 'Weight score' -xmin -5 -xsize 800 -xgstep1 5 -xgstep2 1 -hline red 100 -hline violet 0 -vline violet 5 -ycol 11 -yleg1 'Binomial significance of hit number' -ysize 400 -lines -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.png ; 2014-09-06.012203 cat $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/peak-motifs_oligos_8nt_mkv2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_sites.tab > $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/sites/peak-motifs_all_motifs_seqcoord.tab ; 2014-09-06.012206 $RSAT/perl-scripts/text-to-html -font variable -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/reports/peak-motifs_timelog.txt -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/reports/peak-motifs_timelog.html ; peak-motifs -v 1 -title ChIP-seq_FNR_E._coli_tunned_parameters_dyad_summits_50bps -i $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -motif_db regulonDB tf $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -motif_db footprintDB tf $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -scan_markov 1 -task purge,seqlen,composition,disco,merge_words,collect_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN ; Program version 1.256 ; Parameter values ; seq_format fasta ; img_format png ; ref_motifs_format transfac ; purge_match_length 30 ; purge_mismatches 0 ; origin center ; profiles_ci 20 ; profiles_max_graphs 20 ; profiles_strand -1str ; composition_oligo_lengths 1,2 ; profiles_noov -ovlp ; strand -2str ; disco_noov -noov ; oligo_min_len 6 ; oligo_max_len 8 ; patterns_max_rank 100 ; min_ratio 1 ; min_zscore 6 ; min_sig 0 ; oligo_min_mkv 2 ; oligo_max_mkv 2 ; positions_max_graphs 20 ; asmb_toppat 100 ; max_asmb_width 20 ; matrix_nmotifs 5 ; Input files ; motif_db_footprintDB /vh/rsat/rsat/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf ; motif_db_regulonDB /vh/rsat/rsat/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf ; test_seq /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/peak-motifspeak_seq ; Directories ; output /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/ ; oligos_6nt_mkv2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/ ; oligos_7nt_mkv2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/ ; oligos_8nt_mkv2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_8nt_mkv2/ ; dyads_m1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/ ; dyads_m2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/ ; dyads_m3 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/ ; Output files ; 1nt_test_freq /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_freq-1str-ovlp_1nt.tab ; 1nt_test_heatmap /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_heatmap-1str-ovlp_1nt.png ; 1nt_test_inclusive /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_1nt.txt ; 1nt_test_profiles /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab ; 1nt_test_profiles_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.png ; 1nt_test_profiles_index /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20_graph_index.html ; 1nt_test_transitions /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_transitions-1str-ovlp_1nt.tab ; 2nt_test_freq /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_freq-1str-ovlp_2nt.tab ; 2nt_test_heatmap /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_heatmap-1str-ovlp_2nt.png ; 2nt_test_inclusive /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt ; 2nt_test_profiles /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab ; 2nt_test_profiles_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.png ; 2nt_test_profiles_index /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20_graph_index.html ; 2nt_test_transitions /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/composition/peak-motifs_test_transitions-1str-ovlp_2nt.tab ; archive /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/peak-motifs_archive.zip ; dyads /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads.tab ; dyads_2pssm /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm_log.txt ; dyads_asmb /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/dyads/peak-motifs_dyads-2str-noov_3nt_sp0-20_bg_monads_pssm.asmb ; dyads_m1_logo /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_logo.png ; dyads_m1_logo_rc /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_logo_rc.png ; dyads_m1_pssm_enrichment /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.tab ; dyads_m1_pssm_enrichment_png /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_scan_mkv1_enrichment.png ; dyads_m1_pssm_site_distrib /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.tab ; dyads_m1_pssm_site_distrib_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_site_distrib.png ; dyads_m1_pssm_sites /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites.tab ; dyads_m1_pssm_sites_per_peak /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.tab ; dyads_m1_pssm_sites_per_peak_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_sites_per_peak.png ; dyads_m1_tab /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tab ; dyads_m1_tf /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf ; dyads_m1_vs_db_footprintDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_footprintDB.tab ; dyads_m1_vs_db_footprintDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_footprintDB.html ; dyads_m1_vs_db_regulonDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_regulonDB.tab ; dyads_m1_vs_db_regulonDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_regulonDB.html ; dyads_m1_vs_ref /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_ref.tab ; dyads_m1_vs_ref_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_ref.html ; dyads_m2_logo /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_logo.png ; dyads_m2_logo_rc /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_logo_rc.png ; dyads_m2_pssm_enrichment /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.tab ; dyads_m2_pssm_enrichment_png /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_scan_mkv1_enrichment.png ; dyads_m2_pssm_site_distrib /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.tab ; dyads_m2_pssm_site_distrib_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_site_distrib.png ; dyads_m2_pssm_sites /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites.tab ; dyads_m2_pssm_sites_per_peak /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.tab ; dyads_m2_pssm_sites_per_peak_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_sites_per_peak.png ; dyads_m2_tab /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tab ; dyads_m2_tf /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf ; dyads_m2_vs_db_footprintDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB.tab ; dyads_m2_vs_db_footprintDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB.html ; dyads_m2_vs_db_regulonDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_regulonDB.tab ; dyads_m2_vs_db_regulonDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_regulonDB.html ; dyads_m2_vs_ref /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_ref.tab ; dyads_m2_vs_ref_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_ref.html ; dyads_m3_logo /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_logo.png ; dyads_m3_logo_rc /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_logo_rc.png ; dyads_m3_pssm_enrichment /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.tab ; dyads_m3_pssm_enrichment_png /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_scan_mkv1_enrichment.png ; 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motifs_disco_compa /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab ; motifs_disco_compa_alignments_1ton /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab ; motifs_disco_compa_alignments_1ton_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.html ; motifs_disco_compa_gml /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_disco_compa.gml ; motifs_disco_compa_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_disco_compa.html ; motifs_discovered /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf ; motifs_discovered_table /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered_table.tab ; motifs_vs_db_footprintDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB.tab ; motifs_vs_db_footprintDB_alignments_1ton /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB_alignments_1ton.tab ; motifs_vs_db_footprintDB_alignments_1ton_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB_alignments_1ton.html ; motifs_vs_db_footprintDB_gml /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB.gml ; motifs_vs_db_footprintDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB.html ; motifs_vs_db_regulonDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB.tab ; motifs_vs_db_regulonDB_alignments_1ton /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB_alignments_1ton.tab ; motifs_vs_db_regulonDB_alignments_1ton_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB_alignments_1ton.html ; motifs_vs_db_regulonDB_gml /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB.gml ; motifs_vs_db_regulonDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_regulonDB.html ; oligos_6nt_mkv2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2.tab ; oligos_6nt_mkv2_2pssm /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_log.txt ; oligos_6nt_mkv2_asmb /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm.asmb ; oligos_6nt_mkv2_logo /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_logo.png ; oligos_6nt_mkv2_logo_rc /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_logo_rc.png ; oligos_6nt_mkv2_pssm_counts /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices.txt ; oligos_6nt_mkv2_pssm_enrichment /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_scan_mkv1_enrichment.tab ; oligos_6nt_mkv2_pssm_enrichment_png /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_scan_mkv1_enrichment.png ; oligos_6nt_mkv2_pssm_logo1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m1.png ; oligos_6nt_mkv2_pssm_logo2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m2.png ; oligos_6nt_mkv2_pssm_logo3 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m3.png ; oligos_6nt_mkv2_pssm_logo4 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m4.png ; oligos_6nt_mkv2_pssm_logo5 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m5.png ; oligos_6nt_mkv2_pssm_logo_rc1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m1_rc.png ; oligos_6nt_mkv2_pssm_logo_rc2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m2_rc.png ; oligos_6nt_mkv2_pssm_logo_rc3 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m3_rc.png ; oligos_6nt_mkv2_pssm_logo_rc4 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m4_rc.png ; oligos_6nt_mkv2_pssm_logo_rc5 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices_logo_m5_rc.png ; oligos_6nt_mkv2_pssm_sig /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_sig_matrices.tf ; oligos_6nt_mkv2_pssm_site_distrib /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_site_distrib.tab ; oligos_6nt_mkv2_pssm_site_distrib_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_site_distrib.png ; oligos_6nt_mkv2_pssm_sites /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites.tab ; oligos_6nt_mkv2_pssm_sites_per_peak /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites_per_peak.tab ; oligos_6nt_mkv2_pssm_sites_per_peak_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_sites_per_peak.png ; oligos_6nt_mkv2_pssm_tf /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_6nt_mkv2/peak-motifs_oligos-2str-noov_6nt_mkv2_pssm_count_matrices.tf ; oligos_6nt_mkv2_tab /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tab ; oligos_6nt_mkv2_tf /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tf ; oligos_6nt_mkv2_vs_db_footprintDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB.tab ; oligos_6nt_mkv2_vs_db_footprintDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB.html ; oligos_6nt_mkv2_vs_db_regulonDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_regulonDB.tab ; oligos_6nt_mkv2_vs_db_regulonDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_regulonDB.html ; oligos_6nt_mkv2_vs_ref /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_ref.tab ; oligos_6nt_mkv2_vs_ref_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_ref.html ; oligos_7nt_mkv2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2.tab ; oligos_7nt_mkv2_2pssm /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_log.txt ; oligos_7nt_mkv2_asmb /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm.asmb ; oligos_7nt_mkv2_logo /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_logo.png ; oligos_7nt_mkv2_logo_rc /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_logo_rc.png ; oligos_7nt_mkv2_pssm_counts /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices.txt ; oligos_7nt_mkv2_pssm_enrichment /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_scan_mkv1_enrichment.tab ; oligos_7nt_mkv2_pssm_enrichment_png /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_scan_mkv1_enrichment.png ; oligos_7nt_mkv2_pssm_logo1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices_logo_m1.png ; oligos_7nt_mkv2_pssm_logo2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices_logo_m2.png ; oligos_7nt_mkv2_pssm_logo3 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices_logo_m3.png ; oligos_7nt_mkv2_pssm_logo4 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices_logo_m4.png ; oligos_7nt_mkv2_pssm_logo5 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices_logo_m5.png ; oligos_7nt_mkv2_pssm_logo_rc1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices_logo_m1_rc.png ; oligos_7nt_mkv2_pssm_logo_rc2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices_logo_m2_rc.png ; oligos_7nt_mkv2_pssm_logo_rc3 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices_logo_m3_rc.png ; 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oligos_7nt_mkv2_pssm_sites /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites.tab ; oligos_7nt_mkv2_pssm_sites_per_peak /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites_per_peak.tab ; oligos_7nt_mkv2_pssm_sites_per_peak_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_sites_per_peak.png ; oligos_7nt_mkv2_pssm_tf /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices.tf ; oligos_7nt_mkv2_tab /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tab ; oligos_7nt_mkv2_tf /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2.tf ; oligos_7nt_mkv2_vs_db_footprintDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB.tab ; oligos_7nt_mkv2_vs_db_footprintDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_footprintDB.html ; oligos_7nt_mkv2_vs_db_regulonDB /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_regulonDB.tab ; oligos_7nt_mkv2_vs_db_regulonDB_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_db_regulonDB.html ; oligos_7nt_mkv2_vs_ref /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_ref.tab ; oligos_7nt_mkv2_vs_ref_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_7nt_mkv2/peak-motifs_oligos_7nt_mkv2_vs_ref.html ; oligos_8nt_mkv2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2.tab ; oligos_8nt_mkv2_2pssm /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2_pssm_log.txt ; oligos_8nt_mkv2_asmb /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/oligos_8nt_mkv2/peak-motifs_oligos-2str-noov_8nt_mkv2_pssm.asmb ; 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positions_6nt_pssm_tf /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50_pssm_count_matrices.tf ; positions_7nt /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab ; positions_7nt_2pssm /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_log.txt ; positions_7nt_asmb /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm.asmb ; positions_7nt_pssm_counts /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.txt ; positions_7nt_pssm_logo1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m1.png ; positions_7nt_pssm_logo2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m2.png ; positions_7nt_pssm_logo3 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3.png ; positions_7nt_pssm_logo4 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m4.png ; positions_7nt_pssm_logo5 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m5.png ; positions_7nt_pssm_logo_rc1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m1_rc.png ; positions_7nt_pssm_logo_rc2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m2_rc.png ; positions_7nt_pssm_logo_rc3 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m3_rc.png ; positions_7nt_pssm_logo_rc4 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m4_rc.png ; positions_7nt_pssm_logo_rc5 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo_m5_rc.png ; positions_7nt_pssm_sig /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf ; positions_7nt_pssm_tf /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf ; positions_8nt /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab ; positions_8nt_2pssm /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_log.txt ; positions_8nt_asmb /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm.asmb ; positions_8nt_pssm_counts /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices.txt ; positions_8nt_pssm_logo1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m1.png ; positions_8nt_pssm_logo2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m2.png ; positions_8nt_pssm_logo3 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m3.png ; positions_8nt_pssm_logo4 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m4.png ; positions_8nt_pssm_logo5 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m5.png ; positions_8nt_pssm_logo_rc1 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m1_rc.png ; positions_8nt_pssm_logo_rc2 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m2_rc.png ; positions_8nt_pssm_logo_rc3 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m3_rc.png ; positions_8nt_pssm_logo_rc4 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m4_rc.png ; positions_8nt_pssm_logo_rc5 /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices_logo_m5_rc.png ; positions_8nt_pssm_sig /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_sig_matrices.tf ; positions_8nt_pssm_tf /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50_pssm_count_matrices.tf ; small_summary /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/peak-motifs_small_summary.html ; small_summary_txt /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/reports/peak-motifs_small_summary.txt ; synthesis /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/peak-motifs_synthesis.html ; test_converted /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000.fasta ; test_purged /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta ; test_seqlen /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_seqlen.tab ; test_seqlen_distrib /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_seqlen_distrib.tab ; test_seqlen_distrib_graph /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/data/sequences/peak-motifs_test_seqlen_distrib.png ; timelog /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/reports/peak-motifs_timelog.txt ; timelog_html /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/reports/peak-motifs_timelog.html ; timetable /vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/reports/peak-motifs_timetable.txt ; 2014-09-06.012206 (cd $RSAT/public_html/tmp/apache/2014/09/06 ; zip -ryq peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/peak-motifs_archive.zip peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN -x peak-motifs_archive.zip)