# 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.2026-01-25.202113_2026-01-25.202113_GYd2gc/results/discovered_motifs/oligos_6nt_mkv3_m8/peak-motifs_oligos_6nt_mkv3_m8.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.2026-01-25.202113_2026-01-25.202113_GYd2gc/results/discovered_motifs/oligos_6nt_mkv3_m8/peak-motifs_oligos_6nt_mkv3_m8_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8) |  |  |  |
    ; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; smAACTGArw
    ; Alignment reference
    a	21	31	87	89	0	0	0	94	35	37
    c	26	28	0	0	94	0	0	0	11	18
    g	29	20	0	0	0	0	94	0	25	13
    t	18	15	7	5	0	94	0	0	23	26
ovo_rc_shift1 (ovo_rc) |  |  |  |
    ; oligos_6nt_mkv3_m8 versus ovo_rc; m=1/1; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.444501; -TAACrG---
    ; cor=; Ncor=
    a	0	0	13	11.9167	0	4.33333	0	0	0	0
    c	0	1.08333	0	0	13	0	0	0	0	0
    g	0	0	0	0.541667	0	6.5	13	0	0	0
    t	0	11.9167	0	0.541667	0	2.16667	0	0	0	0