# 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_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7.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_7nt_mkv2_m7/peak-motifs_oligos_7nt_mkv2_m7_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m7_shift0 (oligos_7nt_mkv2_m7) |  |  |  |
    ; oligos_7nt_mkv2_m7; m=0 (reference); ncol1=12; shift=0; ncol=12; rrAACGAGAAbg
    ; Alignment reference
    a	15	10	30	36	2	1	33	0	32	32	5	8
    c	9	6	3	1	34	0	1	2	4	2	10	9
    g	10	12	0	0	1	34	2	35	0	3	10	14
    t	3	9	4	0	0	2	1	0	1	0	12	6
MA0508.4_rc_shift5 (PRDM1_rc) |  |  |  |
    ; oligos_7nt_mkv2_m7 versus MA0508.4_rc (PRDM1_rc); m=1/1; ncol2=7; w=0; offset=5; strand=R; shift=5; score=0.485669; -----GAGAAAG
    ; cor=; Ncor=
    a	0	0	0	0	0	660.0	49466.0	432.0	52619.0	50943.0	52905.0	829.0
    c	0	0	0	0	0	290.0	1390.0	207.0	561.0	1011.0	826.0	701.0
    g	0	0	0	0	0	52821.0	1076.0	53465.0	488.0	1346.0	467.0	52752.0
    t	0	0	0	0	0	1710.0	3549.0	1377.0	1813.0	2181.0	1283.0	1199.0