# 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_m3/peak-motifs_oligos_7nt_mkv2_m3.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_m3/peak-motifs_oligos_7nt_mkv2_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3) |  |  |  |
    ; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwTATATATAww
    ; Alignment reference
    a	0	0	36	33	9	64	4	65	0	58	1	52	22	19
    c	0	0	6	4	3	0	1	1	0	3	1	2	7	5
    g	0	0	5	7	2	1	3	0	1	1	0	3	4	6
    t	0	0	19	22	52	1	58	0	65	4	64	9	33	36
MA0108.3_shift6 (TBP) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus MA0108.3 (TBP); m=1/2; ncol2=7; w=0; offset=4; strand=D; shift=6; score=0.495954; ------TATAWAw-
    ; cor=; Ncor=
    a	0	0	0	0	0	0	16.0	352.0	3.0	354.0	268.0	360.0	222.0	0
    c	0	0	0	0	0	0	46.0	0.0	10.0	0.0	0.0	3.0	2.0	0
    g	0	0	0	0	0	0	18.0	2.0	2.0	5.0	0.0	20.0	44.0	0
    t	0	0	0	0	0	0	309.0	35.0	374.0	30.0	121.0	6.0	121.0	0
MA1974.2_rc_shift0 (ZNF211_rc) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus MA1974.2_rc (ZNF211_rc); m=2/2; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.411296; rTGGTATATr----
    ; cor=; Ncor=
    a	412.0	41.0	38.0	8.0	7.0	776.0	2.0	769.0	3.0	393.0	0	0	0	0
    c	44.0	20.0	5.0	7.0	6.0	3.0	7.0	5.0	13.0	83.0	0	0	0	0
    g	262.0	21.0	741.0	776.0	7.0	11.0	4.0	17.0	21.0	275.0	0	0	0	0
    t	76.0	712.0	10.0	3.0	774.0	4.0	781.0	3.0	757.0	43.0	0	0	0	0