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_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1.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_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift4 ; 15 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)     
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wwTATTCAAww
; Alignment reference
a	0	0	0	0	3011	3222	156	8486	325	665	859	7531	6655	3080	2708
c	0	0	0	0	1346	1211	62	36	294	201	6497	329	495	1408	1628
g	0	0	0	0	1526	1427	76	57	224	322	197	60	385	1305	1259
t	0	0	0	0	2774	2797	8363	78	7814	7469	1104	737	1122	2864	3062
MA0627.3_shift6 (POU2F3) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0627.3 (POU2F3); m=1/14; ncol2=9; w=0; offset=2; strand=D; shift=6; score=0.600187; ------tATGCAAAT
; cor=; Ncor=
a	0	0	0	0	0	0	8522.0	54550.0	1090.0	980.0	946.0	54915.0	51382.0	55302.0	5115.0
c	0	0	0	0	0	0	6885.0	194.0	322.0	251.0	50288.0	80.0	567.0	164.0	3478.0
g	0	0	0	0	0	0	3029.0	354.0	1251.0	51971.0	1079.0	138.0	804.0	233.0	4098.0
t	0	0	0	0	0	0	37593.0	931.0	53366.0	2827.0	3716.0	896.0	3276.0	330.0	43338.0
MA0043.4_shift5 (HLF) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0043.4 (HLF); m=2/14; ncol2=9; w=0; offset=1; strand=D; shift=5; score=0.599602; -----TTATGYAAy-
; cor=; Ncor=
a	0	0	0	0	0	295.0	162.0	22746.0	197.0	2418.0	369.0	24156.0	24055.0	1399.0	0
c	0	0	0	0	0	242.0	96.0	125.0	1548.0	112.0	17203.0	122.0	67.0	13237.0	0
g	0	0	0	0	0	148.0	895.0	1344.0	253.0	21705.0	199.0	48.0	189.0	3300.0	0
t	0	0	0	0	0	23739.0	23271.0	209.0	22426.0	189.0	6653.0	98.0	113.0	6488.0	0
MA0792.1_shift6 (POU5F1B) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0792.1 (POU5F1B); m=3/14; ncol2=9; w=0; offset=2; strand=D; shift=6; score=0.598129; ------TATGywAAT
; cor=; Ncor=
a	0	0	0	0	0	0	1326.0	9519.0	171.0	322.0	398.0	6299.0	9519.0	9519.0	1559.0
c	0	0	0	0	0	0	1778.0	21.0	364.0	94.0	9519.0	51.0	144.0	65.0	537.0
g	0	0	0	0	0	0	808.0	67.0	206.0	9519.0	1293.0	65.0	856.0	97.0	750.0
t	0	0	0	0	0	0	9519.0	84.0	9519.0	1790.0	3828.0	3220.0	896.0	203.0	9519.0
MA0025.3_shift5 (NFIL3) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0025.3 (NFIL3); m=4/14; ncol2=9; w=0; offset=1; strand=D; shift=5; score=0.597425; -----TTATGyAAt-
; cor=; Ncor=
a	0	0	0	0	0	870.0	468.0	21353.0	659.0	1460.0	1358.0	21848.0	21911.0	2193.0	0
c	0	0	0	0	0	681.0	208.0	220.0	1511.0	467.0	12004.0	543.0	251.0	4959.0	0
g	0	0	0	0	0	518.0	1714.0	990.0	492.0	20459.0	454.0	171.0	360.0	2701.0	0
t	0	0	0	0	0	20927.0	20606.0	433.0	20334.0	610.0	9180.0	434.0	474.0	13143.0	0
MA0785.2_shift6 (POU2F1) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0785.2 (POU2F1); m=5/14; ncol2=9; w=0; offset=2; strand=D; shift=6; score=0.593732; ------TATGcwAAT
; cor=; Ncor=
a	0	0	0	0	0	0	756.0	10582.0	153.0	186.0	300.0	6932.0	10582.0	10582.0	1422.0
c	0	0	0	0	0	0	1347.0	12.0	501.0	82.0	10582.0	33.0	108.0	37.0	457.0
g	0	0	0	0	0	0	474.0	29.0	213.0	10582.0	1351.0	46.0	879.0	51.0	755.0
t	0	0	0	0	0	0	10582.0	43.0	10582.0	1326.0	3375.0	3651.0	787.0	158.0	10582.0
MA0784.3_rc_shift4 (POU1F1_rc) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0784.3_rc (POU1F1_rc); m=6/14; ncol2=14; w=0; offset=0; strand=R; shift=4; score=0.55575; ----awTATGCwAAT
; cor=; Ncor=
a	0	0	0	0	3278.0	1804.0	59.0	4127.0	17.0	3.0	16.0	2563.0	4127.0	4127.0	31.0
c	0	0	0	0	384.0	57.0	5.0	0.0	5.0	1.0	3708.0	0.0	2.0	1.0	28.0
g	0	0	0	0	702.0	165.0	5.0	3.0	9.0	4127.0	67.0	0.0	13.0	0.0	7.0
t	0	0	0	0	849.0	2323.0	4127.0	3.0	4127.0	54.0	419.0	1564.0	91.0	0.0	4127.0
MA0619.2_rc_shift7 (LIN54_rc) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0619.2_rc (LIN54_rc); m=7/14; ncol2=7; w=0; offset=3; strand=R; shift=7; score=0.547541; -------ATTyAAA-
; cor=; Ncor=
a	0	0	0	0	0	0	0	685.0	0.0	0.0	0.0	788.0	999.0	999.0	0
c	0	0	0	0	0	0	0	0.0	0.0	0.0	562.0	0.0	0.0	0.0	0
g	0	0	0	0	0	0	0	211.0	0.0	0.0	0.0	212.0	0.0	0.0	0
t	0	0	0	0	0	0	0	104.0	999.0	999.0	438.0	0.0	0.0	0.0	0
MA0507.3_shift5 (POU2F2) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0507.3 (POU2F2); m=8/14; ncol2=13; w=0; offset=1; strand=D; shift=5; score=0.520855; -----wTATGCAAAT
; cor=; Ncor=
a	0	0	0	0	0	5892.0	34.0	9207.0	0.0	0.0	2.0	7279.0	9207.0	9207.0	56.0
c	0	0	0	0	0	435.0	100.0	0.0	13.0	0.0	8014.0	0.0	7.0	5.0	8.0
g	0	0	0	0	0	2020.0	4.0	0.0	2.0	9207.0	127.0	0.0	23.0	0.0	35.0
t	0	0	0	0	0	3315.0	9207.0	0.0	9207.0	111.0	1193.0	1929.0	57.0	8.0	9207.0
MA1115.2_shift7 (POU5F1) 
; oligos_6nt_test_vs_ctrl_m1 versus MA1115.2 (POU5F1); m=9/14; ncol2=7; w=0; offset=3; strand=D; shift=7; score=0.469156; -------ATGCAAA-
; cor=; Ncor=
a	0	0	0	0	0	0	0	12693.0	83.0	717.0	533.0	11756.0	10560.0	12280.0	0
c	0	0	0	0	0	0	0	122.0	130.0	192.0	10310.0	132.0	690.0	270.0	0
g	0	0	0	0	0	0	0	229.0	67.0	11571.0	548.0	118.0	1026.0	257.0	0
t	0	0	0	0	0	0	0	70.0	12834.0	634.0	1723.0	1108.0	838.0	307.0	0
MA0909.4_rc_shift4 (Hoxd13_rc) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0909.4_rc (Hoxd13_rc); m=10/14; ncol2=7; w=0; offset=0; strand=R; shift=4; score=0.447851; ----TTTATTG----
; cor=; Ncor=
a	0	0	0	0	667.0	15.0	11.0	5972.0	30.0	49.0	61.0	0	0	0	0
c	0	0	0	0	379.0	2.0	7.0	3.0	11.0	148.0	34.0	0	0	0	0
g	0	0	0	0	704.0	37.0	4.0	2.0	13.0	5.0	5866.0	0	0	0	0
t	0	0	0	0	4227.0	5923.0	5955.0	0.0	5923.0	5775.0	16.0	0	0	0	0
MA0790.2_rc_shift0 (POU4F1_rc) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0790.2_rc (POU4F1_rc); m=11/14; ncol2=12; w=-4; offset=-4; strand=R; shift=0; score=0.445366; ATtAATwATkcA---
; cor=; Ncor=
a	3102.0	15.0	1116.0	3218.0	3201.0	638.0	1316.0	3511.0	139.0	76.0	750.0	3553.0	0	0	0
c	220.0	54.0	696.0	262.0	129.0	144.0	145.0	15.0	25.0	29.0	3857.0	125.0	0	0	0
g	359.0	36.0	668.0	72.0	106.0	124.0	102.0	15.0	47.0	1661.0	376.0	236.0	0	0	0
t	276.0	3181.0	2825.0	390.0	465.0	2915.0	2811.0	91.0	2950.0	1720.0	1032.0	153.0	0	0	0
MA0602.2_rc_shift3 (Arid5a_rc) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0602.2_rc (Arid5a_rc); m=12/14; ncol2=8; w=-1; offset=-1; strand=R; shift=3; score=0.44401; ---cAATATTr----
; cor=; Ncor=
a	0	0	0	22.0	83.0	96.0	6.0	93.0	2.0	5.0	48.0	0	0	0	0
c	0	0	0	52.0	4.0	1.0	1.0	1.0	1.0	7.0	3.0	0	0	0	0
g	0	0	0	3.0	9.0	1.0	1.0	0.0	0.0	3.0	32.0	0	0	0	0
t	0	0	0	23.0	4.0	2.0	93.0	6.0	96.0	85.0	16.0	0	0	0	0
MA0791.2_rc_shift0 (POU4F3_rc) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0791.2_rc (POU4F3_rc); m=13/14; ncol2=12; w=-4; offset=-4; strand=R; shift=0; score=0.435694; ATtAATwATkcA---
; cor=; Ncor=
a	3774.0	22.0	868.0	3728.0	3805.0	658.0	1579.0	4004.0	132.0	69.0	1067.0	4134.0	0	0	0
c	180.0	25.0	789.0	194.0	166.0	126.0	133.0	25.0	36.0	24.0	4723.0	303.0	0	0	0
g	355.0	19.0	651.0	66.0	101.0	121.0	126.0	21.0	42.0	2014.0	374.0	321.0	0	0	0
t	212.0	3447.0	3100.0	479.0	433.0	3106.0	3041.0	96.0	3264.0	1868.0	1067.0	292.0	0	0	0
MA0151.1_shift7 (Arid3a) 
; oligos_6nt_test_vs_ctrl_m1 versus MA0151.1 (Arid3a); m=14/14; ncol2=6; w=0; offset=3; strand=D; shift=7; score=0.415438; -------ATyAAA--
; cor=; Ncor=
a	0	0	0	0	0	0	0	27.0	0.0	1.0	27.0	27.0	20.0	0	0
c	0	0	0	0	0	0	0	0.0	0.0	9.0	0.0	0.0	0.0	0	0
g	0	0	0	0	0	0	0	0.0	0.0	0.0	0.0	0.0	1.0	0	0
t	0	0	0	0	0	0	0	0.0	27.0	17.0	0.0	0.0	6.0	0	0