# One-to-n alignments

    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_m4/peak-motifs_oligos_6nt_mkv3_m4.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_m4/peak-motifs_oligos_6nt_mkv3_m4_vs_db_Homer

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4) |  |  |  |
    ; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; ssGCGCCGCss
    ; Alignment reference
    a	41	47	7	8	8	8	9	13	13	35	35
    c	132	113	34	279	46	250	253	21	255	141	114
    g	93	100	254	18	243	42	39	261	31	102	109
    t	42	48	13	3	11	8	7	13	9	30	50
homer_266_Sp1_shift1 (homer_266_Sp1) |  |  |  |
    ; oligos_6nt_mkv3_m4 versus homer_266_Sp1; m=1/1; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.611456; -gGCCCCGCCC
    ; cor=; Ncor=
    a	0	18.1	5	1.3	3.3	4.9	0.1	2.5	0.1	0.1	0.1
    c	0	21.8	0.1	87	81.5	94.9	99.7	0.1	99.7	99.7	88.1
    g	0	54.1	94.8	6.1	0.1	0.1	0.1	97.3	0.1	0.1	0.1
    t	0	6	0.1	5.6	15.1	0.1	0.1	0.1	0.1	0.1	11.7