# 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_7nt_mkv2_m1/peak-motifs_oligos_7nt_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_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=20; shift=0; ncol=20; cmmsCCGCsGCSGCGGskkk
    ; Alignment reference
    a	22	33	25	16	11	12	8	2	2	4	1	1	2	2	3	4	1	2	10	10
    c	40	35	54	41	69	66	7	83	61	2	83	26	5	74	8	7	32	10	14	18
    g	19	13	10	34	7	10	74	5	27	84	2	63	82	9	68	69	42	53	35	40
    t	10	10	2	0	4	3	2	1	1	1	5	1	2	6	12	11	16	26	32	23
MA1721.2_shift2 (ZNF93) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus MA1721.2 (ZNF93); m=1/1; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.499926; --gGyrkCrGCAGCGG----
    ; cor=; Ncor=
    a	0	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	0
    c	0	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	0
    g	0	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	0
    t	0	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	0