# 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_m9/peak-motifs_oligos_7nt_mkv5_m9.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_m9/peak-motifs_oligos_7nt_mkv5_m9_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m9_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv5_m9_shift2 (oligos_7nt_mkv5_m9) |  |  |  |
    ; oligos_7nt_mkv5_m9; m=0 (reference); ncol1=13; shift=2; ncol=15; --caCAsACACAAam
    ; Alignment reference
    a	0	0	440	976	136	1526	103	1791	52	1809	40	1764	1473	795	494
    c	0	0	845	301	1425	176	472	44	1715	23	1761	36	298	432	796
    g	0	0	315	389	183	111	1213	34	68	39	57	49	71	334	324
    t	0	0	284	218	140	71	96	15	49	13	26	35	42	323	270
CG13897_SANGER_5_FBgn0035160_shift0 (CG13897_SANGER_5_FBgn0035160) |  |  |  |
    ; oligos_7nt_mkv5_m9 versus CG13897_SANGER_5_FBgn0035160; m=1/2; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.527934; wsrrCAGACAs----
    ; cor=; Ncor=
    a	5	2	8	9	0	17	0	17	0	17	4	0	0	0	0
    c	4	8	0	0	13	0	0	0	17	0	8	0	0	0	0
    g	0	7	8	7	4	0	17	0	0	0	5	0	0	0	0
    t	8	0	1	1	0	0	0	0	0	0	0	0	0	0	0
CG5953_SANGER_5_FBgn0032587_shift3 (CG5953_SANGER_5_FBgn0032587) |  |  |  |
    ; oligos_7nt_mkv5_m9 versus CG5953_SANGER_5_FBgn0032587; m=2/2; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.452834; ---aCAAACAy----
    ; cor=; Ncor=
    a	0	0	0	10	0	16	16	16	0	16	1	0	0	0	0
    c	0	0	0	3	16	0	0	0	16	0	5	0	0	0	0
    g	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
    t	0	0	0	3	0	0	0	0	0	0	10	0	0	0	0