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_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2.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_m2/peak-motifs_oligos_7nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift2 ; 6 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)     
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=2; ncol=17; --aaAAAAAmAAAAAaa
; Alignment reference
a	0	0	8028	8188	13312	13832	14137	13872	14043	6486	14133	13586	14092	13827	13220	8209	8190
c	0	0	1918	2290	713	580	506	432	476	6797	474	624	475	609	856	2147	2174
g	0	0	1989	1821	475	568	347	420	366	857	195	708	388	401	497	2110	2070
t	0	0	3422	3058	857	377	367	633	472	1217	555	439	402	520	784	2891	2923
MA1623.2_shift5 (Stat2) 
; oligos_7nt_test_vs_ctrl_m2 versus MA1623.2 (Stat2); m=1/5; ncol2=10; w=0; offset=3; strand=D; shift=5; score=0.507141; -----gAAACAGAAA--
; cor=; Ncor=
a	0	0	0	0	0	969.0	3554.0	3736.0	3738.0	286.0	3146.0	152.0	3700.0	3747.0	3514.0	0	0
c	0	0	0	0	0	306.0	76.0	75.0	72.0	2907.0	151.0	45.0	49.0	45.0	147.0	0	0
g	0	0	0	0	0	2287.0	168.0	71.0	87.0	524.0	74.0	3707.0	163.0	98.0	157.0	0	0
t	0	0	0	0	0	397.0	161.0	77.0	62.0	242.0	588.0	55.0	47.0	69.0	141.0	0	0
MA1125.2_shift9 (ZNF384) 
; oligos_7nt_test_vs_ctrl_m2 versus MA1125.2 (ZNF384); m=2/5; ncol2=8; w=0; offset=7; strand=D; shift=9; score=0.502369; ---------AAAAAAaa
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	0	30354.0	30191.0	30072.0	30252.0	30202.0	30406.0	20322.0	18916.0
c	0	0	0	0	0	0	0	0	0	7.0	35.0	21.0	13.0	26.0	6.0	2908.0	3963.0
g	0	0	0	0	0	0	0	0	0	13.0	19.0	26.0	15.0	14.0	0.0	2767.0	2898.0
t	0	0	0	0	0	0	0	0	0	59.0	188.0	314.0	153.0	191.0	21.0	4436.0	4656.0
MA1487.3_shift0 (FOXE1) 
; oligos_7nt_test_vs_ctrl_m2 versus MA1487.3 (FOXE1); m=3/5; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.473728; yTAARyAAACAa-----
; cor=; Ncor=
a	86.0	581.0	3126.0	2547.0	2255.0	587.0	3126.0	3126.0	3126.0	0.0	3126.0	2026.0	0	0	0	0	0
c	1646.0	43.0	28.0	113.0	117.0	1062.0	362.0	90.0	0.0	3126.0	32.0	392.0	0	0	0	0	0
g	57.0	0.0	402.0	116.0	871.0	17.0	0.0	0.0	23.0	0.0	18.0	258.0	0	0	0	0	0
t	1479.0	2545.0	43.0	579.0	27.0	2064.0	20.0	53.0	9.0	85.0	110.0	450.0	0	0	0	0	0
MA0847.4_shift0 (FOXD2) 
; oligos_7nt_test_vs_ctrl_m2 versus MA0847.4 (FOXD2); m=4/5; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.402256; yTAAryAAACA------
; cor=; Ncor=
a	219.0	480.0	2484.0	2484.0	2484.0	84.0	2484.0	2484.0	2484.0	0.0	2484.0	0	0	0	0	0	0
c	906.0	19.0	16.0	285.0	23.0	1342.0	81.0	23.0	0.0	2484.0	24.0	0	0	0	0	0	0
g	131.0	0.0	137.0	292.0	1615.0	3.0	0.0	18.0	5.0	0.0	34.0	0	0	0	0	0	0
t	1578.0	2004.0	0.0	262.0	4.0	1141.0	79.0	1.0	2.0	768.0	232.0	0	0	0	0	0	0
MA2124.1_rc_shift2 (Hmga1_rc) 
; oligos_7nt_test_vs_ctrl_m2 versus MA2124.1_rc (Hmga1_rc); m=5/5; ncol2=8; w=0; offset=0; strand=R; shift=2; score=0.401711; --wTAAAAAT-------
; cor=; Ncor=
a	0	0	11340.0	542.0	24333.0	24654.0	24779.0	24269.0	24172.0	496.0	0	0	0	0	0	0	0
c	0	0	2438.0	358.0	294.0	237.0	138.0	303.0	421.0	188.0	0	0	0	0	0	0	0
g	0	0	2348.0	473.0	409.0	264.0	194.0	200.0	393.0	71.0	0	0	0	0	0	0	0
t	0	0	9680.0	24433.0	770.0	651.0	695.0	1034.0	820.0	25051.0	0	0	0	0	0	0	0