# 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.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/oligos_6nt_mkv1_m1/peak-motifs_oligos_6nt_mkv1_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.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/oligos_6nt_mkv1_m1/peak-motifs_oligos_6nt_mkv1_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; mAGCCAGCCAGCC
    ; Alignment reference
    a	32	59	1	1	1	63	1	0	0	62	1	2	3
    c	33	0	8	62	63	1	8	65	63	0	0	58	58
    g	0	5	56	1	0	0	56	0	1	3	64	4	3
    t	0	1	0	1	1	1	0	0	1	0	0	1	1
MA2341.1_shift2 (FEZF2) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus MA2341.1 (FEZF2); m=1/1; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.432688; --CCCAGCCT---
    ; cor=; Ncor=
    a	0	0	17.0	5.0	4.0	231.0	6.0	8.0	7.0	14.0	0	0	0
    c	0	0	202.0	206.0	258.0	15.0	8.0	224.0	247.0	10.0	0	0	0
    g	0	0	10.0	9.0	0.0	14.0	251.0	28.0	2.0	8.0	0	0	0
    t	0	0	36.0	45.0	3.0	5.0	0.0	5.0	9.0	233.0	0	0	0