# 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_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_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_7nt_mkv4_m2/peak-motifs_oligos_7nt_mkv4_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift2 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2) |  |  |  |
    ; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --syGTAGACTAcs
    ; Alignment reference
    a	0	0	49	62	17	6	238	3	200	7	9	224	38	59
    c	0	0	81	75	39	10	10	13	17	239	15	9	117	66
    g	0	0	70	55	182	7	9	242	15	14	6	24	64	80
    t	0	0	64	72	26	241	7	6	32	4	234	7	45	59
MA1602.2_rc_shift0 (ZSCAN29_rc) |  |  |  |
    ; oligos_7nt_mkv4_m2 versus MA1602.2_rc (ZSCAN29_rc); m=1/1; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.499598; CyGyGTAGACr---
    ; cor=; Ncor=
    a	44.0	175.0	12.0	0.0	155.0	4.0	949.0	0.0	977.0	0.0	310.0	0	0	0
    c	786.0	310.0	24.0	350.0	0.0	0.0	0.0	0.0	4.0	977.0	124.0	0	0	0
    g	40.0	207.0	961.0	0.0	838.0	4.0	48.0	993.0	16.0	0.0	497.0	0	0	0
    t	127.0	306.0	0.0	647.0	4.0	989.0	0.0	4.0	0.0	20.0	68.0	0	0	0