# 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_m2/peak-motifs_oligos_7nt_mkv5_m2.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_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_DrosophilaTFs

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2) |  |  |  |
    ; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; hhCCACACCmm
    ; Alignment reference
    a	610	665	56	47	1899	120	1884	31	37	665	597
    c	779	651	2175	2075	185	2039	272	2139	2175	670	740
    g	352	414	33	72	129	81	56	70	39	560	463
    t	597	608	74	144	125	98	126	98	87	443	538
4936_Dip3_DrosophilaTF_1.1__shift2 (4936_Dip3_DrosophilaTF_1.1_) |  |  |  |
    ; oligos_7nt_mkv5_m2 versus 4936_Dip3_DrosophilaTF_1.1_; m=1/1; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.524266; --cCwsrycwk
    ; cor=; Ncor=
    a	0	0	4	4	46	19	35	7	12	35	19
    c	0	0	64	73	11	42	19	58	65	12	8
    g	0	0	8	4	12	31	27	4	4	15	27
    t	0	0	24	19	31	8	19	31	19	38	46