# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_7nt_mkv5_m6/peak-motifs_oligos_7nt_mkv5_m6.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DrosophilaTFs/DrosophilaTFs_2015-11-06.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/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_7nt_mkv5_m6/peak-motifs_oligos_7nt_mkv5_m6_vs_db_DrosophilaTFs

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv5_m6_shift0 (oligos_7nt_mkv5_m6) |  |  |  |
    ; oligos_7nt_mkv5_m6; m=0 (reference); ncol1=17; shift=0; ncol=17; tgsTGCTGyTGCTGytg
    ; Alignment reference
    a	167	226	113	47	59	58	27	40	40	30	21	38	39	45	109	190	250
    c	335	230	1115	82	31	1919	38	44	1312	37	40	1972	68	82	1155	261	291
    g	355	1425	770	45	2066	113	50	2073	102	35	2098	89	51	2015	200	279	1342
    t	1343	319	202	2026	44	110	2085	43	746	2098	41	101	2042	58	736	1470	317
4933_Adf1_DrosophilaTF_1.1__shift4 (4933_Adf1_DrosophilaTF_1.1_) |  |  |  |
    ; oligos_7nt_mkv5_m6 versus 4933_Adf1_DrosophilaTF_1.1_; m=1/1; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.568981; ----GCTsCykCyGyh-
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	0
    c	0	0	0	0	0	1	0	50	1	50	0	1	50	0	50	33	0
    g	0	0	0	0	1	0	0	50	0	0	50	0	0	1	0	0	0
    t	0	0	0	0	0	0	1	0	0	50	50	0	50	0	50	33	0