# 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_m10/peak-motifs_oligos_7nt_mkv5_m10.tf -format2 tf -file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.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_m10/peak-motifs_oligos_7nt_mkv5_m10_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m10_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv5_m10_shift4 (oligos_7nt_mkv5_m10) |  |  |  |
    ; oligos_7nt_mkv5_m10; m=0 (reference); ncol1=11; shift=4; ncol=15; ----rrCAGAGACrg
    ; Alignment reference
    a	0	0	0	0	510	713	119	1668	35	1626	74	1599	123	732	432
    c	0	0	0	0	439	367	1422	60	33	93	37	80	1348	348	434
    g	0	0	0	0	525	496	207	55	1666	59	1613	85	267	487	665
    t	0	0	0	0	329	227	55	20	69	25	79	39	65	236	272
Adf1_SANGER_5_FBgn0000054_shift0 (Adf1_SANGER_5_FBgn0000054) |  |  |  |
    ; oligos_7nt_mkv5_m10 versus Adf1_SANGER_5_FBgn0000054; m=1/3; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.582795; ymcmRGCAGAGmhrm
    ; cor=; Ncor=
    a	1	7	2	4	3	0	0	11	0	8	0	7	4	5	7
    c	5	3	6	7	0	0	11	0	1	1	0	3	4	2	4
    g	0	1	2	0	8	10	0	0	10	2	11	1	0	3	0
    t	5	0	1	0	0	1	0	0	0	0	0	0	3	1	0
CG13897_SANGER_5_FBgn0035160_shift2 (CG13897_SANGER_5_FBgn0035160) |  |  |  |
    ; oligos_7nt_mkv5_m10 versus CG13897_SANGER_5_FBgn0035160; m=2/3; ncol2=11; w=-2; offset=-2; strand=D; shift=2; score=0.514126; --wsrrCAGACAs--
    ; cor=; Ncor=
    a	0	0	5	2	8	9	0	17	0	17	0	17	4	0	0
    c	0	0	4	8	0	0	13	0	0	0	17	0	8	0	0
    g	0	0	0	7	8	7	4	0	17	0	0	0	5	0	0
    t	0	0	8	0	1	1	0	0	0	0	0	0	0	0	0
bin_FlyReg_FBgn0045759_shift2 (bin_FlyReg_FBgn0045759) |  |  |  |
    ; oligos_7nt_mkv5_m10 versus bin_FlyReg_FBgn0045759; m=3/3; ncol2=10; w=-2; offset=-2; strand=D; shift=2; score=0.463785; --TAAACArmGA---
    ; cor=; Ncor=
    a	0	0	0	4	4	4	0	5	3	2	0	4	0	0	0
    c	0	0	0	0	0	1	5	0	0	2	0	0	0	0	0
    g	0	0	0	0	0	0	0	0	2	1	5	1	0	0	0
    t	0	0	5	1	1	0	0	0	0	0	0	0	0	0	0