compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/Homer/Homer_motifs.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/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer Program version 1.118 Quick mode Input files file2 $RSAT/public_html/motif_databases/Homer/Homer_motifs.tf file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.tf Output files alignments_1ton $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer_alignments_1ton.tab alignments_1ton_html $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer_alignments_1ton.html html_index $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer_index.html prefix $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer match_table_txt $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer.tab match_table_html $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer.html Matrices file1 1 matrices $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.tf file1 1 15 291 file2 332 matrices $RSAT/public_html/motif_databases/Homer/Homer_motifs.tf file2 1 14 100.1 file2 2 10 100.1 file2 3 10 100.1 file2 4 15 289 file2 5 20 293.29 file2 6 20 625.62 file2 7 15 481.01 file2 8 8 4075.01 file2 9 10 100.1 file2 10 10 100 file2 11 10 100 ... 322 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_6nt_mkv3_m3 | homer_266_Sp1 | oligos_6nt_mkv3_m3 | homer_266_Sp1 | 0.887 | 0.710 | 15 | 12 | 12 | 15 | 0.8000 | 0.8000 | 1.0000 | D | 2 |
| oligos_6nt_mkv3_m3 | homer_146_KLF3 | oligos_6nt_mkv3_m3 | homer_146_KLF3 | 0.794 | 0.694 | 15 | 15 | 14 | 16 | 0.8750 | 0.9333 | 0.9333 | D | 1 |
| oligos_6nt_mkv3_m3 | homer_145_KLF14 | oligos_6nt_mkv3_m3 | homer_145_KLF14 | 0.835 | 0.668 | 15 | 12 | 12 | 15 | 0.8000 | 0.8000 | 1.0000 | R | 3 |
| oligos_6nt_mkv3_m3 | homer_149_Klf9 | oligos_6nt_mkv3_m3 | homer_149_Klf9 | 0.755 | 0.604 | 15 | 12 | 12 | 15 | 0.8000 | 0.8000 | 1.0000 | D | 3 |
| oligos_6nt_mkv3_m3 | homer_148_KLF5 | oligos_6nt_mkv3_m3 | homer_148_KLF5 | 0.830 | 0.553 | 15 | 10 | 10 | 15 | 0.6667 | 0.6667 | 1.0000 | R | 3 |
| oligos_6nt_mkv3_m3 | homer_160_Maz | oligos_6nt_mkv3_m3 | homer_160_Maz | 0.882 | 0.470 | 15 | 8 | 8 | 15 | 0.5333 | 0.5333 | 1.0000 | R | 4 |
| oligos_6nt_mkv3_m3 | homer_63_Egr2 | oligos_6nt_mkv3_m3 | homer_63_Egr2 | 0.724 | 0.426 | 15 | 12 | 10 | 17 | 0.5882 | 0.6667 | 0.8333 | R | 5 |
Host name rsat Job started 2026-03-30.203915 Job done 2026-03-30.203917 Seconds 0.47 user 0.47 system 0.1 cuser 1.68 ; csystem 0.2