# RSAT - compare-matrices result

### Analysis: result (30/03/2026 20:39)

`Command: 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`

## Input files

Type | File
--- | ---
file1 | peak-motifs_oligos_6nt_mkv3_m3.tf
file2 | ../../../../../../../../../motif_databases/Homer/Homer_motifs.tf

## Output files

Type | File
--- | ---
match_table_txt | peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer.tab
match_table_html | peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer.html
alignments_1ton | peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer_alignments_1ton.tab
alignments_1ton_html | peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer_alignments_1ton.html

## Directories

Type | Directory
--- | ---
output | .
aligned_logos | peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer_aligned_logos