compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3.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/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant Program version 1.118 Quick mode Input files file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3.tf file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt Output files match_table_txt $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.tab alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_alignments_1ton.html match_table_html $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.html alignments_1ton $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_alignments_1ton.tab prefix $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant html_index $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_index.html Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3.tf file1 1 12 16 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_7nt_mkv1_m3 | MA1107.3 | oligos_7nt_mkv1_m3 | KLF9 | 0.734 | 0.673 | 12 | 11 | 11 | 12 | 0.9167 | 0.9167 | 1.0000 | D | 0 |
| oligos_7nt_mkv1_m3 | MA0472.2 | oligos_7nt_mkv1_m3 | EGR2 | 0.778 | 0.599 | 12 | 11 | 10 | 13 | 0.7692 | 0.8333 | 0.9091 | D | -1 |
| oligos_7nt_mkv1_m3 | MA0733.2 | oligos_7nt_mkv1_m3 | EGR4 | 0.774 | 0.595 | 12 | 11 | 10 | 13 | 0.7692 | 0.8333 | 0.9091 | D | -1 |
| oligos_7nt_mkv1_m3 | MA0732.2 | oligos_7nt_mkv1_m3 | EGR3 | 0.771 | 0.593 | 12 | 11 | 10 | 13 | 0.7692 | 0.8333 | 0.9091 | D | -1 |
| oligos_7nt_mkv1_m3 | MA0162.5 | oligos_7nt_mkv1_m3 | EGR1 | 0.766 | 0.531 | 12 | 10 | 9 | 13 | 0.6923 | 0.7500 | 0.9000 | D | -1 |
| oligos_7nt_mkv1_m3 | MA0632.3 | oligos_7nt_mkv1_m3 | TCFL5 | 0.744 | 0.496 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | D | 1 |
| oligos_7nt_mkv1_m3 | MA1512.2 | oligos_7nt_mkv1_m3 | KLF11 | 0.701 | 0.486 | 12 | 10 | 9 | 13 | 0.6923 | 0.7500 | 0.9000 | D | 3 |
| oligos_7nt_mkv1_m3 | MA1099.3 | oligos_7nt_mkv1_m3 | HES1 | 0.728 | 0.485 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | R | 4 |
| oligos_7nt_mkv1_m3 | MA0006.2 | oligos_7nt_mkv1_m3 | Ahr::Arnt | 0.991 | 0.413 | 12 | 5 | 5 | 12 | 0.4167 | 0.4167 | 1.0000 | R | 4 |
| oligos_7nt_mkv1_m3 | MA0039.5 | oligos_7nt_mkv1_m3 | KLF4 | 0.745 | 0.401 | 12 | 8 | 7 | 13 | 0.5385 | 0.5833 | 0.8750 | D | -1 |
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