# 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_m4/peak-motifs_oligos_6nt_mkv4_m4.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_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_DrosophilaTFs

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4) |  |  |  |
    ; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; ammAACACCmc
    ; Alignment reference
    a	603	434	886	1461	1470	34	1378	0	0	542	381
    c	379	473	435	6	49	1453	126	1550	1575	416	540
    g	284	341	132	31	32	32	22	11	3	328	294
    t	322	340	135	90	37	69	62	27	10	302	373
4954_br-Z4_DrosophilaTF_1.1__shift0 (4954_br-Z4_DrosophilaTF_1.1_) |  |  |  |
    ; oligos_6nt_mkv4_m4 versus 4954_br-Z4_DrosophilaTF_1.1_; m=1/1; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.517034; rkAAAsA----
    ; cor=; Ncor=
    a	50	0	1	1	1	0	1	0	0	0	0
    c	0	0	0	0	0	50	0	0	0	0	0
    g	50	50	0	0	0	50	0	0	0	0	0
    t	0	50	0	0	0	0	0	0	0	0	0