# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_7nt_mkv5_m7/peak-motifs_oligos_7nt_mkv5_m7.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_7nt_mkv5_m7/peak-motifs_oligos_7nt_mkv5_m7_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv5_m7_shift0 (oligos_7nt_mkv5_m7) |  |  |  |
    ; oligos_7nt_mkv5_m7; m=0 (reference); ncol1=14; shift=0; ncol=14; ctCTCTyTCTCTCt
    ; Alignment reference
    a	503	585	161	215	120	150	166	109	121	141	154	241	435	595
    c	4268	736	5741	282	5809	301	4049	266	5870	243	5779	444	4387	960
    g	471	820	143	252	136	244	156	293	76	286	147	332	524	719
    t	1206	4307	403	5699	383	5753	2077	5780	381	5778	368	5431	1102	4174
Trl_shift1 (Trl) |  |  |  |
    ; oligos_7nt_mkv5_m7 versus Trl; m=1/1; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.726651; -TtkykCTCtCtct
    ; cor=; Ncor=
    a	0	10	15	4	0	7	0	4	2	6	13	9	4	18
    c	0	10	8	19	41	3	72	0	56	12	56	16	47	3
    g	0	0	13	24	10	27	5	11	8	9	1	6	9	14
    t	0	57	41	30	26	40	0	62	11	50	7	46	17	42