# 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.2026-03-19.143247_2026-03-19.143247_dTipSp/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8.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.2026-03-19.143247_2026-03-19.143247_dTipSp/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: dyads_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m8_shift0 (dyads_m8) |  |  |  |
    ; dyads_m8; m=0 (reference); ncol1=19; shift=0; ncol=19; wwTTAAAAAgAAAwAawww
    ; Alignment reference
    a	85	93	47	18	201	190	198	195	201	48	167	166	194	67	172	150	59	91	86
    c	30	25	11	5	7	5	1	8	3	14	12	16	5	9	10	15	20	18	30
    g	23	25	7	5	2	3	14	6	4	119	10	6	10	9	14	20	22	42	29
    t	83	78	156	193	11	23	8	12	13	40	32	33	12	136	25	36	120	70	76
MA0757.2_shift4 (ONECUT3) |  |  |  |
    ; dyads_m8 versus MA0757.2 (ONECUT3); m=1/1; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.465872; ----aAAAATCrATAa---
    ; cor=; Ncor=
    a	0	0	0	0	3851.0	6080.0	6080.0	6080.0	6080.0	32.0	23.0	3950.0	6080.0	43.0	6080.0	3620.0	0	0	0
    c	0	0	0	0	379.0	274.0	173.0	28.0	5.0	103.0	6080.0	20.0	6.0	6.0	105.0	861.0	0	0	0
    g	0	0	0	0	1141.0	498.0	112.0	102.0	41.0	14.0	3.0	2130.0	9.0	7.0	187.0	417.0	0	0	0
    t	0	0	0	0	709.0	878.0	1221.0	54.0	11.0	6080.0	5.0	11.0	22.0	6080.0	345.0	1182.0	0	0	0