compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2.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/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2_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/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2.tf Output files match_table_txt $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2_vs_db_footprintDB-plants.tab html_index $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2_vs_db_footprintDB-plants_index.html alignments_1ton $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2_vs_db_footprintDB-plants_alignments_1ton.tab prefix $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2_vs_db_footprintDB-plants match_table_html $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2_vs_db_footprintDB-plants.html alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2_vs_db_footprintDB-plants_alignments_1ton.html Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085330_2025-06-19.085330_NC5YGx/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2.tf file1 1 13 3 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| oligos_6-8nt_m2 | TRP5/MA1802.1/JASPAR | oligos_6-8nt_m2 | TRP5:MA1802.1:JASPAR | 0.783 | 0.603 | 13 | 10 | 10 | 13 | 0.7692 | 0.7692 | 1.0000 | R | 2 |
| oligos_6-8nt_m2 | HAT3.1/M0847_1.02/CISBP | oligos_6-8nt_m2 | HAT3.1:M0847_1.02:CISBP | 0.748 | 0.576 | 13 | 10 | 10 | 13 | 0.7692 | 0.7692 | 1.0000 | R | 1 |
| oligos_6-8nt_m2 | Probable/6j4f_F/3D-footprint | oligos_6-8nt_m2 | Probable:6j4f_F:3D-footprint | 0.757 | 0.466 | 13 | 8 | 8 | 13 | 0.6154 | 0.6154 | 1.0000 | D | 4 |
| oligos_6-8nt_m2 | TRP5/MA1802.2/JASPAR | oligos_6-8nt_m2 | TRP5:MA1802.2:JASPAR | 0.851 | 0.458 | 13 | 7 | 7 | 13 | 0.5385 | 0.5385 | 1.0000 | R | 3 |
| oligos_6-8nt_m2 | MYB3/MA1038.2/JASPAR | oligos_6-8nt_m2 | MYB3:MA1038.2:JASPAR | 0.704 | 0.433 | 13 | 8 | 8 | 13 | 0.6154 | 0.6154 | 1.0000 | D | 0 |
| oligos_6-8nt_m2 | RAP2-7/MA1796.1/JASPAR | oligos_6-8nt_m2 | RAP2-7:MA1796.1:JASPAR | 0.844 | 0.422 | 13 | 8 | 7 | 14 | 0.5000 | 0.5385 | 0.8750 | D | -1 |
Host name rsat Job started 2025-06-19.085345 Job done 2025-06-19.085347 Seconds 1.22 user 1.22 system 0.07 cuser 0.23 ; csystem 0.04