# 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.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8.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.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m8_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m8_shift1 (dyads_m8) |  |  |  |
    ; dyads_m8; m=0 (reference); ncol1=10; shift=1; ncol=11; -ykGCCACCrm
    ; Alignment reference
    a	0	536	670	67	33	0	2893	0	0	886	857
    c	0	837	665	49	2834	2835	0	2896	2885	527	828
    g	0	619	804	2757	3	1	0	0	1	782	661
    t	0	904	757	23	26	60	3	0	10	701	550
brk_shift0 (brk) |  |  |  |
    ; dyads_m8 versus brk; m=1/1; ncol2=7; w=-1; offset=-1; strand=D; shift=0; score=0.401047; rGCGCCr----
    ; cor=; Ncor=
    a	4.4	2.2	0	0	0	0	5.5	0	0	0	0
    c	0	0	9.9	0	11	11	0	0	0	0	0
    g	6.6	8.8	0	9.9	0	0	5.5	0	0	0	0
    t	0	0	1.1	1.1	0	0	0	0	0	0	0