# 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.2025-05-16.184046_2025-05-16.184046_ZEi16E/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.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.2025-05-16.184046_2025-05-16.184046_ZEi16E/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5) |  |  |  |
    ; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ykCTACTMArwr
    ; Alignment reference
    a	2	1	0	0	9	0	0	8	11	7	6	5
    c	5	2	11	1	0	10	0	3	0	0	1	1
    g	1	3	0	0	1	1	0	0	0	3	1	4
    t	3	5	0	10	1	0	11	0	0	1	3	1
MA1645.2_shift2 (NKX2-2) |  |  |  |
    ; oligos_7nt_mkv2_m5 versus MA1645.2 (NKX2-2); m=1/2; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.467383; --CCACTCAA--
    ; cor=; Ncor=
    a	0	0	2438.0	618.0	23748.0	478.0	490.0	397.0	21326.0	20003.0	0	0
    c	0	0	20232.0	24341.0	463.0	24693.0	452.0	24058.0	2772.0	2104.0	0	0
    g	0	0	2293.0	176.0	257.0	420.0	295.0	838.0	580.0	2266.0	0	0
    t	0	0	1060.0	888.0	1555.0	432.0	24786.0	730.0	1345.0	1650.0	0	0
MA1963.2_shift2 (SATB1) |  |  |  |
    ; oligos_7nt_mkv2_m5 versus MA1963.2 (SATB1); m=2/2; ncol2=7; w=0; offset=2; strand=D; shift=2; score=0.457639; --CTAATAA---
    ; cor=; Ncor=
    a	0	0	262.0	492.0	33670.0	32708.0	288.0	32009.0	30660.0	0	0	0
    c	0	0	33122.0	195.0	164.0	115.0	128.0	485.0	881.0	0	0	0
    g	0	0	140.0	37.0	221.0	120.0	123.0	889.0	1071.0	0	0	0
    t	0	0	700.0	33500.0	169.0	1281.0	33685.0	841.0	1612.0	0	0	0