# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184201_2025-05-16.184201_aBOVlS/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2025/05/16/peak-motifs.2025-05-16.184201_2025-05-16.184201_aBOVlS/results/discovered_motifs/oligos_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=18; shift=0; ncol=18; mmsCCGCSGCSGCGGskk
    ; Alignment reference
    a	37	37	22	20	18	5	2	2	6	4	0	3	1	3	4	3	5	15
    c	34	40	40	69	69	4	87	71	1	88	25	6	88	8	4	32	15	12
    g	13	16	33	6	8	88	6	25	90	1	71	87	4	72	74	44	43	35
    t	14	5	3	3	3	1	3	0	1	5	2	2	5	15	16	19	35	36
MA1721.2_shift1 (ZNF93) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus MA1721.2 (ZNF93); m=1/1; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.559418; -gGyrkCrGCAGCGG---
    ; cor=; Ncor=
    a	0	467.0	175.0	117.0	1455.0	61.0	38.0	1001.0	18.0	23.0	1659.0	30.0	19.0	340.0	72.0	0	0	0
    c	0	279.0	233.0	1120.0	177.0	114.0	2278.0	92.0	26.0	2279.0	96.0	20.0	2292.0	138.0	134.0	0	0	0
    g	0	1499.0	1857.0	211.0	663.0	1483.0	22.0	1263.0	2334.0	42.0	576.0	2328.0	33.0	1784.0	2145.0	0	0	0
    t	0	143.0	123.0	940.0	93.0	730.0	50.0	32.0	10.0	44.0	57.0	10.0	44.0	126.0	37.0	0	0	0