compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf Output files prefix $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants match_table_txt $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants.tab alignments_1ton $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants_alignments_1ton.tab alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants_alignments_1ton.html match_table_html $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants.html html_index $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants_index.html Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m5/peak-motifs_dyads_m5.tf file1 1 12 60 file2 2958 matrices $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf file2 1 8 5 file2 2 8 3 file2 3 8 5 file2 4 8 1 file2 5 8 2 file2 6 8 2 file2 7 8 6 file2 8 8 2 file2 9 8 8 file2 10 8 1 file2 11 8 4 ... 2948 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_m5 | HMG-1/MA0044.1/JASPAR | dyads_m5 | HMG-1:MA0044.1:JASPAR | 0.768 | 0.576 | 12 | 9 | 9 | 12 | 0.7500 | 0.7500 | 1.0000 | R | 3 |
| dyads_m5 | EDF3/M0080_1.02/CISBP | dyads_m5 | EDF3:M0080_1.02:CISBP | 0.703 | 0.469 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | D | 4 |
| dyads_m5 | REM1/UN0407.2/JASPAR | dyads_m5 | REM1:UN0407.2:JASPAR | 0.739 | 0.431 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | R | 5 |
| dyads_m5 | Lysine-specific/6jnm_A/3D-footprint | dyads_m5 | Lysine-specific:6jnm_A:3D-footprint | 0.923 | 0.426 | 12 | 7 | 6 | 13 | 0.4615 | 0.5000 | 0.8571 | R | 6 |
| dyads_m5 | ASIL1/M1618_1.02/CISBP | dyads_m5 | ASIL1:M1618_1.02:CISBP | 0.721 | 0.412 | 12 | 10 | 8 | 14 | 0.5714 | 0.6667 | 0.8000 | D | -2 |
| dyads_m5 | CRL1BOX/EEAD0081/EEADannot | dyads_m5 | CRL1BOX:EEAD0081:EEADannot | 0.810 | 0.405 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 6 |
| dyads_m5 | Lysine-specific/6jnn_B/3D-footprint | dyads_m5 | Lysine-specific:6jnn_B:3D-footprint | 0.809 | 0.404 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 6 |
Host name rsat Job started 2025-05-21.034024 Job done 2025-05-21.034026 Seconds 1.29 user 1.29 system 0.04 cuser 0.2 ; csystem 0.03