# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_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/2026/01/05/peak-motifs.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6nt_m3_shift0 (positions_6nt_m3) |  |  |  |
    ; positions_6nt_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; awAcATATATgTwt
    ; Alignment reference
    a	4863	3175	10539	1420	11163	1114	9757	1021	9453	467	2247	619	4059	3027
    c	1852	2994	433	8000	252	922	573	847	709	316	531	607	1970	2456
    g	2456	1970	607	531	316	709	847	573	922	252	8000	433	2994	1852
    t	3027	4059	619	2247	467	9453	1021	9757	1114	11163	1420	10539	3175	4863
MA0461.3_shift1 (Atoh1) |  |  |  |
    ; positions_6nt_m3 versus MA0461.3 (Atoh1); m=1/1; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.41037; -rmCATATG-----
    ; cor=; Ncor=
    a	0	655.0	523.0	42.0	1027.0	17.0	1027.0	22.0	2.0	0	0	0	0	0
    c	0	108.0	334.0	1027.0	20.0	10.0	74.0	4.0	1.0	0	0	0	0	0
    g	0	372.0	149.0	8.0	34.0	136.0	0.0	5.0	1027.0	0	0	0	0	0
    t	0	59.0	21.0	0.0	0.0	1027.0	0.0	1027.0	31.0	0	0	0	0	0