# 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/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.2026-01-25.180905_2026-01-25.180905_kvVFaU/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; -rtATAGGAww
    ; Alignment reference
    a	0	170	118	470	0	527	4	9	441	146	185
    c	0	110	78	26	1	3	18	0	4	98	104
    g	0	138	114	34	14	4	489	429	35	128	95
    t	0	116	224	4	519	0	23	96	54	162	150
br-Z2_rc_shift0 (br-Z2_rc) |  |  |  |
    ; positions_6-8nt_m1 versus br-Z2_rc; m=1/1; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.498118; twaaTAG----
    ; cor=; Ncor=
    a	5	9	12	11	0	21	1	0	0	0	0
    c	4	1	3	3	0	0	0	0	0	0	0
    g	0	3	1	3	0	0	20	0	0	0	0
    t	12	8	5	4	21	0	0	0	0	0	0