compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.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 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22_vs_db_jaspar_core_nonredundant_vertebrates Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf file1 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22.tf Output files alignments_1ton Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22_vs_db_jaspar_core_nonredundant_vertebrates_alignments_1ton.tab match_table_txt Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22_vs_db_jaspar_core_nonredundant_vertebrates.tab html_index Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22_vs_db_jaspar_core_nonredundant_vertebrates_index.html alignments_1ton_html Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22_vs_db_jaspar_core_nonredundant_vertebrates_alignments_1ton.html match_table_html Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22_vs_db_jaspar_core_nonredundant_vertebrates.html prefix Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22_vs_db_jaspar_core_nonredundant_vertebrates Matrices file1 1 matrices Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m22/peak-motifs_dyads_m22.tf file1 1 10 21 file2 746 matrices $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf file2 1 6 24 file2 2 17 100 file2 3 10 9897 file2 4 17 101 file2 5 17 3851 file2 6 10 25318 file2 7 6 27 file2 8 11 1001 file2 9 14 101 file2 10 6 20 file2 11 8 104 ... 736 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| dyads_m22 | MA0461.2 | dyads_m22dyads_m22 | Atoh1 | 0.772 | 0.772 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA1638.1 | dyads_m22dyads_m22 | HAND2 | 0.758 | 0.758 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA0633.1 | dyads_m22dyads_m22 | Twist2 | 0.756 | 0.756 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | R | 0 |
| dyads_m22 | MA1108.2 | dyads_m22dyads_m22 | MXI1 | 0.752 | 0.752 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA1468.1 | dyads_m22dyads_m22 | ATOH7 | 0.747 | 0.747 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA0818.1 | dyads_m22dyads_m22 | BHLHE22 | 0.745 | 0.745 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA1570.1 | dyads_m22dyads_m22 | TFAP4(var.2) | 0.742 | 0.742 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | R | 0 |
| dyads_m22 | MA0100.3 | dyads_m22dyads_m22 | MYB | 0.741 | 0.741 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA0826.1 | dyads_m22dyads_m22 | OLIG1 | 0.741 | 0.741 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA0827.1 | dyads_m22dyads_m22 | OLIG3 | 0.736 | 0.736 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA0678.1 | dyads_m22dyads_m22 | OLIG2 | 0.734 | 0.734 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA0669.1 | dyads_m22dyads_m22 | NEUROG2 | 0.727 | 0.727 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA0623.2 | dyads_m22dyads_m22 | NEUROG1 | 0.727 | 0.727 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | D | 0 |
| dyads_m22 | MA0668.1 | dyads_m22dyads_m22 | NEUROD2 | 0.716 | 0.716 | 10 | 10 | 10 | 10 | 1.0000 | 1.0000 | 1.0000 | R | 0 |
| dyads_m22 | MA1524.1 | dyads_m22dyads_m22 | MSGN1 | 0.817 | 0.681 | 10 | 12 | 10 | 12 | 0.8333 | 1.0000 | 0.8333 | R | -1 |
| dyads_m22 | MA0607.1 | dyads_m22dyads_m22 | Bhlha15 | 0.778 | 0.622 | 10 | 8 | 8 | 10 | 0.8000 | 0.8000 | 1.0000 | R | 1 |
| dyads_m22 | MA0817.1 | dyads_m22dyads_m22 | BHLHE23 | 0.743 | 0.619 | 10 | 12 | 10 | 12 | 0.8333 | 1.0000 | 0.8333 | D | -1 |
| dyads_m22 | MA0091.1 | dyads_m22dyads_m22 | TAL1::TCF3 | 0.719 | 0.599 | 10 | 12 | 10 | 12 | 0.8333 | 1.0000 | 0.8333 | R | 0 |
| dyads_m22 | MA1568.1 | dyads_m22dyads_m22 | TCF21(var.2) | 0.709 | 0.591 | 10 | 12 | 10 | 12 | 0.8333 | 1.0000 | 0.8333 | R | -1 |
| dyads_m22 | MA1642.1 | dyads_m22dyads_m22 | NEUROG2(var.2) | 0.751 | 0.577 | 10 | 13 | 10 | 13 | 0.7692 | 1.0000 | 0.7692 | D | -2 |
| dyads_m22 | MA1618.1 | dyads_m22dyads_m22 | Ptf1a | 0.737 | 0.567 | 10 | 13 | 10 | 13 | 0.7692 | 1.0000 | 0.7692 | D | -1 |
| dyads_m22 | MA1123.2 | dyads_m22dyads_m22 | TWIST1 | 0.726 | 0.558 | 10 | 13 | 10 | 13 | 0.7692 | 1.0000 | 0.7692 | D | -2 |
| dyads_m22 | MA1109.1 | dyads_m22dyads_m22 | NEUROD1 | 0.714 | 0.549 | 10 | 13 | 10 | 13 | 0.7692 | 1.0000 | 0.7692 | D | -1 |
| dyads_m22 | MA0507.1 | dyads_m22dyads_m22 | POU2F2 | 0.709 | 0.545 | 10 | 13 | 10 | 13 | 0.7692 | 1.0000 | 0.7692 | R | -3 |
| dyads_m22 | MA0514.1 | dyads_m22dyads_m22 | Sox3 | 0.731 | 0.487 | 10 | 10 | 8 | 12 | 0.6667 | 0.8000 | 0.8000 | R | -2 |
| dyads_m22 | MA0792.1 | dyads_m22dyads_m22 | POU5F1B | 0.718 | 0.419 | 10 | 9 | 7 | 12 | 0.5833 | 0.7000 | 0.7778 | D | -2 |
| dyads_m22 | MA0789.1 | dyads_m22dyads_m22 | POU3F4 | 0.701 | 0.409 | 10 | 9 | 7 | 12 | 0.5833 | 0.7000 | 0.7778 | D | -2 |
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