# 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.2026-01-25.181000_2026-01-25.181000_CpuIe4/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.2026-01-25.181000_2026-01-25.181000_CpuIe4/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_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m8_shift1 (oligos_6-8nt_m8) |  |  |  |
    ; oligos_6-8nt_m8; m=0 (reference); ncol1=11; shift=1; ncol=12; -cbCTCTCCCtc
    ; Alignment reference
    a	0	771	701	108	155	94	158	79	156	194	1015	646
    c	0	1663	1103	3887	116	3844	138	3643	3109	3671	904	1769
    g	0	795	1185	74	218	132	245	288	360	206	912	914
    t	0	999	1239	159	3739	158	3687	218	603	157	1397	899
Trl_shift0 (Trl) |  |  |  |
    ; oligos_6-8nt_m8 versus Trl; m=1/1; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.652055; TtkykCTCtCtc
    ; cor=; Ncor=
    a	10	15	4	0	7	0	4	2	6	13	9	4
    c	10	8	19	41	3	72	0	56	12	56	16	47
    g	0	13	24	10	27	5	11	8	9	1	6	9
    t	57	41	30	26	40	0	62	11	50	7	46	17