compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2.tf Output files prefix $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant html_index $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_index.html match_table_txt $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.tab alignments_1ton $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_alignments_1ton.tab alignments_1ton_html $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_alignments_1ton.html match_table_html $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.html Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2.tf file1 1 13 3409 file2 879 matrices $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt file2 1 6 20 file2 2 14 43 file2 3 10 25 file2 4 15 10 file2 5 10 17 file2 6 10 18 file2 7 17 25 file2 8 15 33 file2 9 14 16 file2 10 6 16 file2 11 15 1369 ... 869 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| oligos_6nt_test_vs_ctrl_m2 | MA1978.2 | oligos_6nt_test_vs_ctrl_m2 | ZNF354A | 0.749 | 0.487 | 13 | 20 | 13 | 20 | 0.6500 | 1.0000 | 0.6500 | D | -3 |
| oligos_6nt_test_vs_ctrl_m2 | MA2124.1 | oligos_6nt_test_vs_ctrl_m2 | Hmga1 | 0.751 | 0.462 | 13 | 8 | 8 | 13 | 0.6154 | 0.6154 | 1.0000 | R | 0 |
| oligos_6nt_test_vs_ctrl_m2 | MA0108.3 | oligos_6nt_test_vs_ctrl_m2 | TBP | 0.849 | 0.457 | 13 | 7 | 7 | 13 | 0.5385 | 0.5385 | 1.0000 | D | 1 |
| oligos_6nt_test_vs_ctrl_m2 | MA1473.2 | oligos_6nt_test_vs_ctrl_m2 | CDX4 | 0.776 | 0.443 | 13 | 9 | 8 | 14 | 0.5714 | 0.6154 | 0.8889 | D | -1 |
| oligos_6nt_test_vs_ctrl_m2 | MA0899.2 | oligos_6nt_test_vs_ctrl_m2 | HOXA10 | 0.756 | 0.432 | 13 | 9 | 8 | 14 | 0.5714 | 0.6154 | 0.8889 | D | -1 |
| oligos_6nt_test_vs_ctrl_m2 | MA0650.4 | oligos_6nt_test_vs_ctrl_m2 | Hoxa13 | 0.859 | 0.430 | 13 | 8 | 7 | 14 | 0.5000 | 0.5385 | 0.8750 | D | -1 |
| oligos_6nt_test_vs_ctrl_m2 | MA0465.3 | oligos_6nt_test_vs_ctrl_m2 | CDX2 | 0.853 | 0.427 | 13 | 8 | 7 | 14 | 0.5000 | 0.5385 | 0.8750 | D | -1 |
| oligos_6nt_test_vs_ctrl_m2 | MA0909.4 | oligos_6nt_test_vs_ctrl_m2 | Hoxd13 | 0.788 | 0.424 | 13 | 7 | 7 | 13 | 0.5385 | 0.5385 | 1.0000 | D | 0 |
| oligos_6nt_test_vs_ctrl_m2 | MA0913.3 | oligos_6nt_test_vs_ctrl_m2 | HOXD9 | 0.735 | 0.420 | 13 | 9 | 8 | 14 | 0.5714 | 0.6154 | 0.8889 | D | -1 |
| oligos_6nt_test_vs_ctrl_m2 | MA0878.3 | oligos_6nt_test_vs_ctrl_m2 | CDX1 | 0.763 | 0.407 | 13 | 10 | 8 | 15 | 0.5333 | 0.6154 | 0.8000 | D | -2 |
| oligos_6nt_test_vs_ctrl_m2 | MA0635.2 | oligos_6nt_test_vs_ctrl_m2 | BARHL2 | 0.870 | 0.401 | 13 | 6 | 6 | 13 | 0.4615 | 0.4615 | 1.0000 | D | 3 |
Host name rsat Job started 2026-01-05.150823 Job done 2026-01-05.150829 Seconds 1.39 user 1.4 system 0.26 cuser 4.69 ; csystem 0.39