# 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.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_motifs/positions_6-8nt_m1/peak-motifs_positions_6-8nt_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.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_motifs/positions_6-8nt_m1/peak-motifs_positions_6-8nt_m1_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_6-8nt_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6-8nt_m1_shift0 (positions_6-8nt_m1) |  |  |  |
    ; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; kyCGCCGCyg
    ; Alignment reference
    a	107	85	0	1	0	0	0	0	88	108
    c	88	148	448	4	448	448	1	448	166	110
    g	137	102	0	434	0	0	443	0	68	137
    t	116	113	0	9	0	0	4	0	126	93
brk_shift0 (brk) |  |  |  |
    ; positions_6-8nt_m1 versus brk; m=1/2; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.580827; rGCGCCr---
    ; cor=; Ncor=
    a	4.4	2.2	0	0	0	0	5.5	0	0	0
    c	0	0	9.9	0	11	11	0	0	0	0
    g	6.6	8.8	0	9.9	0	0	5.5	0	0	0
    t	0	0	1.1	1.1	0	0	0	0	0	0
Mad_shift2 (Mad) |  |  |  |
    ; positions_6-8nt_m1 versus Mad; m=2/2; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.472012; --CGmsrCgm
    ; cor=; Ncor=
    a	0	0	3	1	7	1	6	2	3	6
    c	0	0	15	0	11	7	3	14	1	8
    g	0	0	1	17	1	8	10	0	12	2
    t	0	0	0	1	0	3	0	3	3	3