# 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_7nt_mkv5_m6/peak-motifs_oligos_7nt_mkv5_m6.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.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/oligos_7nt_mkv5_m6/peak-motifs_oligos_7nt_mkv5_m6_vs_db_FlyFactorSurvey

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m6_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv5_m6_shift0 (oligos_7nt_mkv5_m6) |  |  |  |
    ; oligos_7nt_mkv5_m6; m=0 (reference); ncol1=17; shift=0; ncol=17; tgsTGCTGyTGCTGytg
    ; Alignment reference
    a	167	226	113	47	59	58	27	40	40	30	21	38	39	45	109	190	250
    c	335	230	1115	82	31	1919	38	44	1312	37	40	1972	68	82	1155	261	291
    g	355	1425	770	45	2066	113	50	2073	102	35	2098	89	51	2015	200	279	1342
    t	1343	319	202	2026	44	110	2085	43	746	2098	41	101	2042	58	736	1470	317
odd_NAR_FBgn0002985_rc_shift5 (odd_NAR_FBgn0002985_rc) |  |  |  |
    ; oligos_7nt_mkv5_m6 versus odd_NAR_FBgn0002985_rc; m=1/3; ncol2=11; w=0; offset=5; strand=R; shift=5; score=0.459648; -----bTGCTACTGkk-
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	0	0	15	0	0	0	0	3	0
    c	0	0	0	0	0	6	1	0	15	0	0	15	3	1	0	0	0
    g	0	0	0	0	0	4	3	15	0	0	0	0	0	14	5	5	0
    t	0	0	0	0	0	5	11	0	0	15	0	0	12	0	10	7	0
Aef1_SANGER_5_FBgn0005694_rc_shift1 (Aef1_SANGER_5_FBgn0005694_rc) |  |  |  |
    ; oligos_7nt_mkv5_m6 versus Aef1_SANGER_5_FBgn0005694_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.453241; -GKTGTTGTTGy-----
    ; cor=; Ncor=
    a	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
    c	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0
    g	0	9	3	0	12	0	0	12	0	0	12	2	0	0	0	0	0
    t	0	2	9	12	0	12	12	0	12	12	0	6	0	0	0	0	0
CG11504_SANGER_5_FBgn0039733_rc_shift5 (CG11504_SANGER_5_FBgn0039733_rc) |  |  |  |
    ; oligos_7nt_mkv5_m6 versus CG11504_SANGER_5_FBgn0039733_rc; m=3/3; ncol2=9; w=0; offset=5; strand=R; shift=5; score=0.406288; -----ATGTTGCkR---
    ; cor=; Ncor=
    a	0	0	0	0	0	14	0	0	1	0	0	0	3	6	0	0	0
    c	0	0	0	0	0	0	0	0	0	0	0	19	1	0	0	0	0
    g	0	0	0	0	0	4	0	19	0	0	19	1	5	14	0	0	0
    t	0	0	0	0	0	2	20	1	19	20	1	0	11	0	0	0	0