# 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.2026-03-19.135349_2026-03-19.135349_WDqUmM/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6.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.2026-03-19.135349_2026-03-19.135349_WDqUmM/results/discovered_motifs/oligos_6nt_mkv2_m6/peak-motifs_oligos_6nt_mkv2_m6_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m6_shift0 (oligos_6nt_mkv2_m6) |  |  |  |
    ; oligos_6nt_mkv2_m6; m=0 (reference); ncol1=10; shift=0; ncol=10; yaGTACTAcw
    ; Alignment reference
    a	16	30	2	1	73	4	0	73	16	24
    c	19	10	0	0	0	68	0	1	25	9
    g	8	17	69	0	0	0	0	0	15	10
    t	31	17	3	73	1	2	74	0	18	31
MA2336.1_shift0 (ZSCAN21) |  |  |  |
    ; oligos_6nt_mkv2_m6 versus MA2336.1 (ZSCAN21); m=1/1; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.497361; AAGCACT---
    ; cor=; Ncor=
    a	703.0	896.0	28.0	17.0	893.0	25.0	37.0	0	0	0
    c	124.0	16.0	25.0	744.0	21.0	881.0	9.0	0	0	0
    g	55.0	25.0	853.0	32.0	22.0	30.0	16.0	0	0	0
    t	65.0	10.0	41.0	154.0	11.0	11.0	885.0	0	0	0