# 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.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/oligos_6nt_mkv4_m8/peak-motifs_oligos_6nt_mkv4_m8.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.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/oligos_6nt_mkv4_m8/peak-motifs_oligos_6nt_mkv4_m8_vs_db_DrosophilaTFs

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m8_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m8_shift0 (oligos_6nt_mkv4_m8) |  |  |  |
    ; oligos_6nt_mkv4_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; mrCAAAACam
    ; Alignment reference
    a	588	575	0	1505	1527	1517	1531	0	700	535
    c	401	285	1520	0	0	0	0	1533	288	428
    g	275	408	0	3	0	1	0	0	317	327
    t	269	265	13	25	6	15	2	0	228	243
4953_br-Z3_DrosophilaTF_1.1__shift3 (4953_br-Z3_DrosophilaTF_1.1_) |  |  |  |
    ; oligos_6nt_mkv4_m8 versus 4953_br-Z3_DrosophilaTF_1.1_; m=1/2; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.510925; ---wAAACww
    ; cor=; Ncor=
    a	0	0	0	50	1	1	1	0	50	50
    c	0	0	0	0	0	0	0	1	0	0
    g	0	0	0	0	0	0	0	0	0	0
    t	0	0	0	50	0	0	0	0	50	50
4958_croc_DrosophilaTF_1.1__shift1 (4958_croc_DrosophilaTF_1.1_) |  |  |  |
    ; oligos_6nt_mkv4_m8 versus 4958_croc_DrosophilaTF_1.1_; m=2/2; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.422479; -rTAAAA---
    ; cor=; Ncor=
    a	0	67	0	1	1	80	1	0	0	0
    c	0	0	0	0	0	20	0	0	0	0
    g	0	33	0	0	0	0	0	0	0	0
    t	0	0	1	0	0	0	0	0	0	0