# 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_m9/peak-motifs_oligos_6-8nt_m9.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_m9/peak-motifs_oligos_6-8nt_m9_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m9_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m9_shift1 (oligos_6-8nt_m9) |  |  |  |
    ; oligos_6-8nt_m9; m=0 (reference); ncol1=11; shift=1; ncol=12; -ctCCCTCTCyc
    ; Alignment reference
    a	0	663	699	92	206	224	211	67	97	58	630	753
    c	0	1705	928	3668	2848	3367	155	3713	116	3769	1224	1621
    g	0	830	1002	125	388	197	240	107	155	103	915	822
    t	0	847	1416	160	603	257	3439	158	3677	115	1276	849
Trl_shift0 (Trl) |  |  |  |
    ; oligos_6-8nt_m9 versus Trl; m=1/2; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.650596; 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
z_rc_shift5 (z_rc) |  |  |  |
    ; oligos_6-8nt_m9 versus z_rc; m=2/2; ncol2=6; w=0; offset=4; strand=R; shift=5; score=0.426975; -----CaCTCA-
    ; cor=; Ncor=
    a	0	0	0	0	0	5.12195	24.5854	0	0	0	29.7073	0
    c	0	0	0	0	0	30.7317	0	42	0	42	3.07317	0
    g	0	0	0	0	0	5.12195	10.2439	0	0	0	7.17073	0
    t	0	0	0	0	0	1.02439	7.17073	0	42	0	2.04878	0