# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.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/2026/01/25/peak-motifs.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m1_shift0 (dyads_m1) |  |  |  |
    ; dyads_m1; m=0 (reference); ncol1=18; shift=0; ncol=18; gaGrGAGAGrGAGAGrga
    ; Alignment reference
    a	507	1361	325	1047	182	2307	112	2255	163	1039	186	2322	100	2276	243	1032	549	1258
    c	356	421	229	206	121	159	78	161	118	227	78	113	63	155	171	293	347	481
    g	1582	565	1992	1321	2365	191	2500	202	2356	1348	2413	223	2511	190	2177	1252	1561	676
    t	323	421	222	194	100	111	78	150	131	154	91	110	94	147	177	191	311	353
Trl_rc_shift5 (Trl_rc) |  |  |  |
    ; dyads_m1 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=5; strand=R; shift=5; score=0.600661; -----agaGaGAGmrmaA
    ; cor=; Ncor=
    a	0	0	0	0	0	42	17	46	7	50	11	62	0	40	26	30	41	57
    c	0	0	0	0	0	14	9	6	1	9	8	11	5	27	10	24	13	0
    g	0	0	0	0	0	3	47	16	56	12	56	0	72	3	41	19	8	10
    t	0	0	0	0	0	18	4	9	13	6	2	4	0	7	0	4	15	10