# 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.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4.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.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |  |  |  |
    ; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; AwATATAATATAT
    ; Alignment reference
    a	38	14	49	2	46	5	41	41	3	44	5	36	8
    c	1	3	0	1	0	1	1	1	1	1	6	1	6
    g	2	1	1	0	3	0	1	0	1	3	2	7	2
    t	9	32	0	47	1	44	7	8	45	2	37	6	34
MA0108.3_shift1 (TBP) |  |  |  |
    ; oligos_7nt_mkv2_m4 versus MA0108.3 (TBP); m=1/2; ncol2=7; w=0; offset=1; strand=D; shift=1; score=0.469013; -TATAWAw-----
    ; cor=; Ncor=
    a	0	16.0	352.0	3.0	354.0	268.0	360.0	222.0	0	0	0	0	0
    c	0	46.0	0.0	10.0	0.0	0.0	3.0	2.0	0	0	0	0	0
    g	0	18.0	2.0	2.0	5.0	0.0	20.0	44.0	0	0	0	0	0
    t	0	309.0	35.0	374.0	30.0	121.0	6.0	121.0	0	0	0	0	0
MA0602.2_shift5 (Arid5a) |  |  |  |
    ; oligos_7nt_mkv2_m4 versus MA0602.2 (Arid5a); m=2/2; ncol2=8; w=0; offset=5; strand=D; shift=5; score=0.45964; -----yAATATTg
    ; cor=; Ncor=
    a	0	0	0	0	0	16.0	85.0	96.0	6.0	93.0	2.0	4.0	23.0
    c	0	0	0	0	0	32.0	3.0	0.0	0.0	1.0	1.0	9.0	3.0
    g	0	0	0	0	0	3.0	7.0	1.0	1.0	1.0	1.0	4.0	52.0
    t	0	0	0	0	0	48.0	5.0	2.0	93.0	6.0	96.0	83.0	22.0