compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4.tf Output files alignments_1ton_html $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila_alignments_1ton.html match_table_txt $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila.tab alignments_1ton $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila_alignments_1ton.tab html_index $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila_index.html match_table_html $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila.html prefix $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4.tf file1 1 12 5744 file2 41 matrices $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf file2 1 6 45.00005 file2 2 6 18 file2 3 6 14 file2 4 8 49.00004 file2 5 8 18.00005 file2 6 7 21 file2 7 11 16 file2 8 8 8 file2 9 7 11 file2 10 8 10 file2 11 9 13 ... 31 more matrices Column content 1 id1 Identifier of the first matrix 2 id2 Identifier of the second matrix 3 name1 Name of the first matrix 4 name2 Name of the second matrix 5 cor Pearson coefficient of correlation between frequency matrices 6 Ncor Normalized correlation. Ncor = cor * Wr 7 w1 Width of the first matrix 8 w2 Width of the second matrix 9 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset) 10 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w 11 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W 12 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1 13 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2 14 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse) 15 offset shift of the second matrix relative to the first matrix (negative:left; positive: right)
| id1 | id2 | name1 | name2 | cor | Ncor | w1 | w2 | w | W | Wr | wr1 | wr2 | strand | offset |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| positions_6-8nt_m4 | br-Z1 | positions_6-8nt_m4 | br-Z1 | 0.756 | 0.504 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | D | 2 |
| positions_6-8nt_m4 | en | positions_6-8nt_m4 | en | 0.733 | 0.489 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | R | 4 |
| positions_6-8nt_m4 | eve | positions_6-8nt_m4 | eve | 0.726 | 0.484 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | D | 2 |
| positions_6-8nt_m4 | br-Z4 | positions_6-8nt_m4 | br-Z4 | 0.709 | 0.473 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | R | 0 |
| positions_6-8nt_m4 | Antp | positions_6-8nt_m4 | Antp | 0.935 | 0.468 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 5 |
| positions_6-8nt_m4 | ap | positions_6-8nt_m4 | ap | 0.906 | 0.453 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 2 |
| positions_6-8nt_m4 | zen | positions_6-8nt_m4 | zen | 0.894 | 0.447 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 5 |
| positions_6-8nt_m4 | gt | positions_6-8nt_m4 | gt | 0.765 | 0.446 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 0 |
| positions_6-8nt_m4 | abd-A | positions_6-8nt_m4 | abd-A | 0.842 | 0.421 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 6 |
Host name rsat Job started 2026-01-25.181521 Job done 2026-01-25.181523 Seconds 0.25 user 0.25 system 0.08 cuser 1.31 ; csystem 0.22