# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.184326_2026-01-25.184326_ptOhrJ/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.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/2026/01/25/peak-motifs.2026-01-25.184326_2026-01-25.184326_ptOhrJ/results/discovered_motifs/positions_6-8nt_m4/peak-motifs_positions_6-8nt_m4_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6-8nt_m4_shift0 (positions_6-8nt_m4) |  |  |  |
    ; positions_6-8nt_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; ggCGGCGChs
    ; Alignment reference
    a	54	38	0	0	0	0	0	0	62	43
    c	52	41	235	0	0	235	0	235	68	67
    g	86	104	0	235	235	0	235	0	42	82
    t	43	52	0	0	0	0	0	0	63	43
brk_rc_shift2 (brk_rc) |  |  |  |
    ; positions_6-8nt_m4 versus brk_rc; m=1/1; ncol2=7; w=0; offset=2; strand=R; shift=2; score=0.631842; --yGGCGCy-
    ; cor=; Ncor=
    a	0	0	0	0	0	1.1	1.1	0	0	0
    c	0	0	5.5	0	0	9.9	0	8.8	6.6	0
    g	0	0	0	11	11	0	9.9	0	0	0
    t	0	0	5.5	0	0	0	0	2.2	4.4	0