# 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.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/oligos_6-8nt_m8/peak-motifs_oligos_6-8nt_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.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/oligos_6-8nt_m8/peak-motifs_oligos_6-8nt_m8_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8) |  |  |  |
    ; oligos_6-8nt_m8; m=0 (reference); ncol1=11; shift=0; ncol=11; arTAGGAAGwr
    ; Alignment reference
    a	1613	1509	422	4272	283	274	4456	4610	261	1534	1315
    c	1026	1014	477	210	173	174	206	74	142	1092	1105
    g	1163	1321	558	234	4248	4331	130	124	4291	972	1399
    t	1120	1078	3465	206	218	143	130	114	228	1324	1103
Eip74EF_shift2 (Eip74EF) |  |  |  |
    ; oligos_6-8nt_m8 versus Eip74EF; m=1/1; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.589285; --mMGGAAkT-
    ; cor=; Ncor=
    a	0	0	3	6	1	0	8	8	1	1	0
    c	0	0	5	2	0	1	0	0	0	1	0
    g	0	0	0	0	7	7	0	0	5	0	0
    t	0	0	0	0	0	0	0	0	2	6	0