# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135315_2026-03-19.135315_TQdT35/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2.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/2026/03/19/peak-motifs.2026-03-19.135315_2026-03-19.135315_TQdT35/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2) |  |  |  |
    ; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; ssrTGCATGCAbs
    ; Alignment reference
    a	118	121	193	27	22	16	543	5	17	13	464	97	105
    c	152	198	132	43	8	530	12	15	10	517	37	178	150
    g	159	157	151	38	527	9	10	18	527	9	42	144	180
    t	141	94	94	462	13	15	5	532	16	31	27	151	135
MA1115.2_shift6 (POU5F1) |  |  |  |
    ; oligos_6nt_mkv3_m2 versus MA1115.2 (POU5F1); m=1/1; ncol2=7; w=0; offset=6; strand=D; shift=6; score=0.437381; ------ATGCAAA
    ; cor=; Ncor=
    a	0	0	0	0	0	0	12693.0	83.0	717.0	533.0	11756.0	10560.0	12280.0
    c	0	0	0	0	0	0	122.0	130.0	192.0	10310.0	132.0	690.0	270.0
    g	0	0	0	0	0	0	229.0	67.0	11571.0	548.0	118.0	1026.0	257.0
    t	0	0	0	0	0	0	70.0	12834.0	634.0	1723.0	1108.0	838.0	307.0