# 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.2026-01-25.184326_2026-01-25.184326_ptOhrJ/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.2026-01-25.184326_2026-01-25.184326_ptOhrJ/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_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6-8nt_m1_shift1 (positions_6-8nt_m1) |  |  |  |
    ; positions_6-8nt_m1; m=0 (reference); ncol1=10; shift=1; ncol=11; -wyATTTTCww
    ; Alignment reference
    a	0	76	51	279	0	11	7	4	0	87	80
    c	0	61	76	0	0	0	1	0	279	61	61
    g	0	56	57	0	0	0	1	0	0	58	57
    t	0	86	95	0	279	268	270	275	0	73	81
dl_shift0 (dl) |  |  |  |
    ; positions_6-8nt_m1 versus dl; m=1/1; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.654598; kkrwTTTyCym
    ; cor=; Ncor=
    a	0	2	20	13	2	0	2	0	1	0	12
    c	1	3	0	4	0	1	4	21	36	16	17
    g	22	21	18	3	2	3	1	0	0	9	8
    t	15	12	0	18	34	34	31	17	1	13	1