# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2026/01/05/peak-motifs.2026-01-05.145905_2026-01-05.145905_RyN7XF/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=20; shift=0; ncol=20; wwAAAAAgAAAtGAAATgww
    ; Alignment reference
    a	580	560	1051	1053	1120	1101	1083	245	1136	1134	1142	297	251	1135	1110	1139	251	241	573	524
    c	165	173	57	74	48	55	32	73	37	60	62	42	48	44	66	46	62	90	208	221
    g	240	216	91	94	52	70	69	848	69	50	58	124	907	43	62	66	82	823	189	229
    t	337	373	123	101	102	96	138	156	80	78	60	859	116	100	84	71	927	168	352	348
MA1623.2_shift1 (Stat2) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m5 versus MA1623.2 (Stat2); m=1/1; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.42106; -gAAACAGAAA---------
    ; cor=; Ncor=
    a	0	969.0	3554.0	3736.0	3738.0	286.0	3146.0	152.0	3700.0	3747.0	3514.0	0	0	0	0	0	0	0	0	0
    c	0	306.0	76.0	75.0	72.0	2907.0	151.0	45.0	49.0	45.0	147.0	0	0	0	0	0	0	0	0	0
    g	0	2287.0	168.0	71.0	87.0	524.0	74.0	3707.0	163.0	98.0	157.0	0	0	0	0	0	0	0	0	0
    t	0	397.0	161.0	77.0	62.0	242.0	588.0	55.0	47.0	69.0	141.0	0	0	0	0	0	0	0	0	0