# 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_m5/peak-motifs_oligos_6nt_mkv3_m5.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_m5/peak-motifs_oligos_6nt_mkv3_m5_vs_db_Homer

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift3 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5) |  |  |  |
    ; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=3; ncol=13; ---svCGaGCGss
    ; Alignment reference
    a	0	0	0	55	62	14	11	160	7	9	11	52	54
    c	0	0	0	66	69	208	13	26	5	216	11	78	73
    g	0	0	0	81	70	8	219	45	233	13	216	72	77
    t	0	0	0	45	46	17	4	16	2	9	9	45	43
homer_326_ZNF519_shift0 (homer_326_ZNF519) |  |  |  |
    ; oligos_6nt_mkv3_m5 versus homer_326_ZNF519; m=1/1; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.482002; GAGsCCGAGC---
    ; cor=; Ncor=
    a	0.45	443.67	0.45	8.9	4.89	9.35	0.45	424.97	0.45	0.45	0	0	0
    c	0.45	0.45	0.45	214.94	432.99	411.62	29.37	11.12	0.45	432.09	0	0	0
    g	443.67	0.45	443.67	150.86	4.45	0.45	414.74	7.12	441.88	0.45	0	0	0
    t	0.45	0.45	0.45	70.31	2.67	23.59	0.45	1.78	2.23	12.02	0	0	0