# 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.2026-01-25.180905_2026-01-25.180905_kvVFaU/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.2026-01-25.180905_2026-01-25.180905_kvVFaU/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m6_shift0 (dyads_m6) |  |  |  |
    ; dyads_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; gyCGCCGCCGcc
    ; Alignment reference
    a	394	275	67	76	73	57	54	68	61	101	418	352
    c	311	600	1501	24	1551	1549	27	1519	1558	83	634	660
    g	617	420	65	1583	54	19	1622	84	26	1483	360	307
    t	423	450	112	62	67	120	42	74	100	78	333	426
brk_shift0 (brk) |  |  |  |
    ; dyads_m6 versus brk; m=1/2; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.483643; rGCGCCr-----
    ; cor=; Ncor=
    a	4.4	2.2	0	0	0	0	5.5	0	0	0	0	0
    c	0	0	9.9	0	11	11	0	0	0	0	0	0
    g	6.6	8.8	0	9.9	0	0	5.5	0	0	0	0	0
    t	0	0	1.1	1.1	0	0	0	0	0	0	0	0
Med_shift3 (Med) |  |  |  |
    ; dyads_m6 versus Med; m=2/2; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.460441; ---sCmssCsmm
    ; cor=; Ncor=
    a	0	0	0	1	0	5	0	0	0	0	3	4
    c	0	0	0	2	8	3	3	4	7	3	5	4
    g	0	0	0	5	0	0	4	4	1	5	0	0
    t	0	0	0	0	0	0	1	0	0	0	0	0