compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.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.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_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.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.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.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.tab prefix $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_alignments_1ton.html match_table_html $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.html alignments_1ton $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_alignments_1ton.tab html_index $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_index.html Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.tf file1 1 12 80 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_mkv2_m5 | MA1979.2 | oligos_7nt_mkv2_m5 | ZNF416 | 0.712 | 0.594 | 12 | 10 | 10 | 12 | 0.8333 | 0.8333 | 1.0000 | R | 2 |
| oligos_7nt_mkv2_m5 | MA1588.1 | oligos_7nt_mkv2_m5 | ZNF136 | 0.720 | 0.576 | 12 | 15 | 12 | 15 | 0.8000 | 1.0000 | 0.8000 | R | -1 |
| oligos_7nt_mkv2_m5 | MA0161.3 | oligos_7nt_mkv2_m5 | NFIC | 0.866 | 0.505 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | R | 2 |
| oligos_7nt_mkv2_m5 | MA1729.2 | oligos_7nt_mkv2_m5 | ZNF680 | 0.841 | 0.448 | 12 | 11 | 8 | 15 | 0.5333 | 0.6667 | 0.7273 | D | 4 |
| oligos_7nt_mkv2_m5 | MA0671.2 | oligos_7nt_mkv2_m5 | NFIX | 0.888 | 0.444 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 2 |
| oligos_7nt_mkv2_m5 | MA0670.2 | oligos_7nt_mkv2_m5 | NFIA | 0.828 | 0.414 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 2 |
| oligos_7nt_mkv2_m5 | MA0119.1 | oligos_7nt_mkv2_m5 | NFIC::TLX1 | 0.906 | 0.403 | 12 | 14 | 8 | 18 | 0.4444 | 0.6667 | 0.5714 | D | -6 |
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