# 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.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m3/peak-motifs_positions_6-8nt_m3.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.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/positions_6-8nt_m3/peak-motifs_positions_6-8nt_m3_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6-8nt_m3_shift0 (positions_6-8nt_m3) |  |  |  |
    ; positions_6-8nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wwCGTCAAcr
    ; Alignment reference
    a	246	282	0	0	0	0	809	964	223	279
    c	211	209	983	0	0	983	6	9	288	214
    g	243	208	0	983	0	0	29	5	232	265
    t	283	284	0	0	983	0	139	5	240	225
tin_rc_shift4 (tin_rc) |  |  |  |
    ; positions_6-8nt_m3 versus tin_rc; m=1/1; ncol2=7; w=0; offset=4; strand=R; shift=4; score=0.416108; ----TCAAGT
    ; cor=; Ncor=
    a	0	0	0	0	0	0	11	11	0	0
    c	0	0	0	0	1	8	0	0	0	0
    g	0	0	0	0	0	1	0	0	11	1
    t	0	0	0	0	10	2	0	0	0	10