# 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_m7/peak-motifs_dyads_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/2026/01/25/peak-motifs.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m7_shift0 (dyads_m7) |  |  |  |
    ; dyads_m7; m=0 (reference); ncol1=10; shift=0; ncol=10; ygCCGCCGmc
    ; Alignment reference
    a	516	670	7	1	41	29	3	4	730	692
    c	903	398	2819	2827	22	2775	2826	0	961	1043
    g	624	1071	0	2	2713	1	2	2816	573	474
    t	789	693	6	2	56	27	1	12	568	623
brk_shift1 (brk) |  |  |  |
    ; dyads_m7 versus brk; m=1/1; ncol2=7; w=0; offset=1; strand=D; shift=1; score=0.496144; -rGCGCCr--
    ; cor=; Ncor=
    a	0	4.4	2.2	0	0	0	0	5.5	0	0
    c	0	0	0	9.9	0	11	11	0	0	0
    g	0	6.6	8.8	0	9.9	0	0	5.5	0	0
    t	0	0	0	1.1	1.1	0	0	0	0	0