compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_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/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_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/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5.tf Output files html_index $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants_index.html alignments_1ton_html $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants_alignments_1ton.html match_table_html $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants.html prefix $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants alignments_1ton $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants_alignments_1ton.tab match_table_txt $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants.tab Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5.tf file1 1 11 45 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_m5 | E2Fc/E2Fc/Athamap | oligos_6-8nt_m5 | E2Fc:E2Fc:Athamap | 0.828 | 0.573 | 11 | 11 | 9 | 13 | 0.6923 | 0.8182 | 0.8182 | D | 2 |
| oligos_6-8nt_m5 | E2Fa/E2Fa/Athamap | oligos_6-8nt_m5 | E2Fa:E2Fa:Athamap | 0.770 | 0.560 | 11 | 8 | 8 | 11 | 0.7273 | 0.7273 | 1.0000 | D | 1 |
| oligos_6-8nt_m5 | E2Fb/E2Fb/Athamap | oligos_6-8nt_m5 | E2Fb:E2Fb:Athamap | 0.767 | 0.558 | 11 | 8 | 8 | 11 | 0.7273 | 0.7273 | 1.0000 | D | 1 |
| oligos_6-8nt_m5 | NID1/MA1793.2/JASPAR | oligos_6-8nt_m5 | NID1:MA1793.2:JASPAR | 0.881 | 0.480 | 11 | 6 | 6 | 11 | 0.5455 | 0.5455 | 1.0000 | D | 0 |
| oligos_6-8nt_m5 | TIFY2A/M0760_1.02/CISBP | oligos_6-8nt_m5 | TIFY2A:M0760_1.02:CISBP | 0.711 | 0.452 | 11 | 7 | 7 | 11 | 0.6364 | 0.6364 | 1.0000 | R | 0 |
| oligos_6-8nt_m5 | AT4G09450/MA2103.1/JASPAR | oligos_6-8nt_m5 | AT4G09450:MA2103.1:JASPAR | 0.823 | 0.449 | 11 | 6 | 6 | 11 | 0.5455 | 0.5455 | 1.0000 | D | 0 |
| oligos_6-8nt_m5 | fgenesh1_pg.scaffold_70000111/M1388_1.02/CISBP | oligos_6-8nt_m5 | fgenesh1_pg.scaffold_70000111:M1388_1.02:CISBP | 0.820 | 0.442 | 11 | 9 | 7 | 13 | 0.5385 | 0.6364 | 0.7778 | R | -2 |
| oligos_6-8nt_m5 | AT5G08520/M1339_1.02/CISBP | oligos_6-8nt_m5 | AT5G08520:M1339_1.02:CISBP | 0.764 | 0.411 | 11 | 9 | 7 | 13 | 0.5385 | 0.6364 | 0.7778 | R | -2 |
| oligos_6-8nt_m5 | GATA8/MA1017.2/JASPAR | oligos_6-8nt_m5 | GATA8:MA1017.2:JASPAR | 0.884 | 0.402 | 11 | 5 | 5 | 11 | 0.4545 | 0.4545 | 1.0000 | R | 0 |
Host name rsat Job started 2025-06-19.093813 Job done 2025-06-19.093814 Seconds 1.28 user 1.29 system 0.05 cuser 0.21 ; csystem 0.03