# 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_m2/peak-motifs_oligos_6nt_mkv2_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.2026-03-19.135349_2026-03-19.135349_WDqUmM/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; crTGCATGCAyg
    ; Alignment reference
    a	36	58	8	6	10	149	2	7	7	134	27	27
    c	58	26	9	2	135	0	3	2	139	3	43	33
    g	33	43	3	139	2	3	0	135	2	9	26	58
    t	27	27	134	7	7	2	149	10	6	8	58	36
MA1115.2_rc_shift0 (POU5F1_rc) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus MA1115.2_rc (POU5F1_rc); m=1/1; ncol2=7; w=0; offset=0; strand=R; shift=0; score=0.472155; TTTGCAT-----
    ; cor=; Ncor=
    a	307.0	838.0	1108.0	1723.0	634.0	12834.0	70.0	0	0	0	0	0
    c	257.0	1026.0	118.0	548.0	11571.0	67.0	229.0	0	0	0	0	0
    g	270.0	690.0	132.0	10310.0	192.0	130.0	122.0	0	0	0	0	0
    t	12280.0	10560.0	11756.0	533.0	717.0	83.0	12693.0	0	0	0	0	0