# 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_m6/peak-motifs_dyads_m6.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_m6/peak-motifs_dyads_m6_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m6_shift0 (dyads_m6) |  |  |  |
    ; dyads_m6; m=0 (reference); ncol1=19; shift=0; ncol=19; yyCTCycyctcyytCTCyy
    ; Alignment reference
    a	1234	1346	250	300	260	949	1219	1142	978	1283	1032	1107	1080	1378	263	324	237	1046	1262
    c	2778	1785	6311	282	6363	1861	2924	1985	3414	1345	3531	1896	3039	1702	6302	292	6387	1894	2699
    g	1006	1168	214	132	154	1289	1075	989	1196	986	1026	1355	955	1050	217	154	150	1300	1115
    t	1889	2608	132	6193	130	2808	1689	2791	1319	3293	1318	2549	1833	2777	125	6137	133	2667	1831
Trl_shift5 (Trl) |  |  |  |
    ; dyads_m6 versus Trl; m=1/1; ncol2=13; w=0; offset=5; strand=D; shift=5; score=0.484162; -----TtkykCTCtCtct-
    ; cor=; Ncor=
    a	0	0	0	0	0	10	15	4	0	7	0	4	2	6	13	9	4	18	0
    c	0	0	0	0	0	10	8	19	41	3	72	0	56	12	56	16	47	3	0
    g	0	0	0	0	0	0	13	24	10	27	5	11	8	9	1	6	9	14	0
    t	0	0	0	0	0	57	41	30	26	40	0	62	11	50	7	46	17	42	0