# 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_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.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_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_DrosophilaTFs

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1) |  |  |  |
    ; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; cycCCACAAmm
    ; Alignment reference
    a	354	335	306	0	2	1250	50	1267	1364	427	379
    c	516	530	804	1437	1382	94	1304	72	17	444	541
    g	254	207	179	0	16	42	44	36	33	264	277
    t	320	372	155	7	44	58	46	69	30	309	247
4934_Aef1_DrosophilaTF_1.1__shift3 (4934_Aef1_DrosophilaTF_1.1_) |  |  |  |
    ; oligos_6nt_mkv4_m1 versus 4934_Aef1_DrosophilaTF_1.1_; m=1/1; ncol2=6; w=0; offset=3; strand=D; shift=3; score=0.415469; ---CAACAA--
    ; cor=; Ncor=
    a	0	0	0	0	1	1	0	1	1	0	0
    c	0	0	0	1	0	0	1	0	0	0	0
    g	0	0	0	0	0	0	0	0	0	0	0
    t	0	0	0	0	0	0	0	0	0	0	0