compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_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/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4_vs_db_JASPAR2024_CORE_plants_non-redundant Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_non-redundant_pfms_transfac.txt file1 $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4.tf Output files html_index $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4_vs_db_JASPAR2024_CORE_plants_non-redundant_index.html alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4_vs_db_JASPAR2024_CORE_plants_non-redundant_alignments_1ton.html alignments_1ton $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4_vs_db_JASPAR2024_CORE_plants_non-redundant_alignments_1ton.tab match_table_html $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4_vs_db_JASPAR2024_CORE_plants_non-redundant.html prefix $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4_vs_db_JASPAR2024_CORE_plants_non-redundant match_table_txt $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4_vs_db_JASPAR2024_CORE_plants_non-redundant.tab Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m4/peak-motifs_oligos_8nt_mkv1_m4.tf file1 1 13 2 file2 805 matrices $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_non-redundant_pfms_transfac.txt file2 1 6 21 file2 2 5 15 file2 3 9 70 file2 4 5 16 file2 5 7 35 file2 6 12 33 file2 7 10 49 file2 8 8 13 file2 9 7 15 file2 10 14 558 file2 11 8 101 ... 795 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_8nt_mkv1_m4 | MA1747.2 | oligos_8nt_mkv1_m4 | DOF4.3 | 0.714 | 0.612 | 13 | 13 | 12 | 14 | 0.8571 | 0.9231 | 0.9231 | R | 1 |
| oligos_8nt_mkv1_m4 | MA2029.2 | oligos_8nt_mkv1_m4 | MYB88 | 0.734 | 0.508 | 13 | 9 | 9 | 13 | 0.6923 | 0.6923 | 1.0000 | D | 3 |
| oligos_8nt_mkv1_m4 | MA0973.2 | oligos_8nt_mkv1_m4 | CDF2 | 0.876 | 0.471 | 13 | 7 | 7 | 13 | 0.5385 | 0.5385 | 1.0000 | D | 0 |
| oligos_8nt_mkv1_m4 | MA1815.2 | oligos_8nt_mkv1_m4 | GRF4 | 0.718 | 0.442 | 13 | 8 | 8 | 13 | 0.6154 | 0.6154 | 1.0000 | R | 5 |
| oligos_8nt_mkv1_m4 | MA1272.3 | oligos_8nt_mkv1_m4 | DOF2.2 | 0.943 | 0.435 | 13 | 6 | 6 | 13 | 0.4615 | 0.4615 | 1.0000 | D | 0 |
| oligos_8nt_mkv1_m4 | MA1280.2 | oligos_8nt_mkv1_m4 | DOF5.4 | 0.800 | 0.431 | 13 | 7 | 7 | 13 | 0.5385 | 0.5385 | 1.0000 | D | 0 |
| oligos_8nt_mkv1_m4 | MA1276.2 | oligos_8nt_mkv1_m4 | DOF3.5 | 0.753 | 0.406 | 13 | 7 | 7 | 13 | 0.5385 | 0.5385 | 1.0000 | D | 0 |
Host name rsat Job started 2025-11-07.144638 Job done 2025-11-07.144640 Seconds 0.42 user 0.42 system 0.08 cuser 1.04 ; csystem 0.16