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.2026-01-05.115003_2026-01-05.115003_UARk68/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.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.2026-01-05.115003_2026-01-05.115003_UARk68/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift6 ; 15 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift6 (oligos_7nt_mkv5_m4)    
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=6; ncol=17; ------bsCGGCTGCsk
; Alignment reference
a	0	0	0	0	0	0	376	343	61	81	70	42	157	63	83	414	398
c	0	0	0	0	0	0	1071	1112	2778	244	514	2843	324	194	2692	1150	751
g	0	0	0	0	0	0	770	1139	118	2607	2340	92	347	2635	117	904	1082
t	0	0	0	0	0	0	791	414	51	76	84	31	2180	116	116	540	777
MA0048.3_shift6 (NHLH1)
; oligos_7nt_mkv5_m4 versus MA0048.3 (NHLH1); m=1/14; ncol2=9; w=0; offset=0; strand=D; shift=6; score=0.60439; ------cGCAGCTGC--
; cor=; Ncor=
a	0	0	0	0	0	0	788.0	461.0	3.0	2166.0	0.0	96.0	0.0	2.0	296.0	0	0
c	0	0	0	0	0	0	2166.0	179.0	2166.0	3.0	301.0	2166.0	4.0	4.0	2166.0	0	0
g	0	0	0	0	0	0	181.0	2166.0	0.0	1.0	2166.0	124.0	4.0	2166.0	102.0	0	0
t	0	0	0	0	0	0	111.0	142.0	0.0	0.0	114.0	0.0	2166.0	1.0	350.0	0	0
MA1721.2_shift3 (ZNF93)
; oligos_7nt_mkv5_m4 versus MA1721.2 (ZNF93); m=2/14; ncol2=14; w=-3; offset=-3; strand=D; shift=3; score=0.568427; ---gGyrkCrGCAGCGG
; cor=; Ncor=
a	0	0	0	467.0	175.0	117.0	1455.0	61.0	38.0	1001.0	18.0	23.0	1659.0	30.0	19.0	340.0	72.0
c	0	0	0	279.0	233.0	1120.0	177.0	114.0	2278.0	92.0	26.0	2279.0	96.0	20.0	2292.0	138.0	134.0
g	0	0	0	1499.0	1857.0	211.0	663.0	1483.0	22.0	1263.0	2334.0	42.0	576.0	2328.0	33.0	1784.0	2145.0
t	0	0	0	143.0	123.0	940.0	93.0	730.0	50.0	32.0	10.0	44.0	57.0	10.0	44.0	126.0	37.0
MA0500.3_shift7 (MYOG)
; oligos_7nt_mkv5_m4 versus MA0500.3 (MYOG); m=3/14; ncol2=8; w=0; offset=1; strand=D; shift=7; score=0.532783; -------rCAGCTGy--
; cor=; Ncor=
a	0	0	0	0	0	0	0	7159.0	86.0	21782.0	95.0	167.0	163.0	182.0	1667.0	0	0
c	0	0	0	0	0	0	0	2730.0	21988.0	176.0	130.0	21964.0	238.0	102.0	10792.0	0	0
g	0	0	0	0	0	0	0	10790.0	101.0	236.0	21963.0	131.0	179.0	21985.0	2706.0	0	0
t	0	0	0	0	0	0	0	1678.0	182.0	163.0	169.0	95.0	21777.0	88.0	7192.0	0	0
MA1728.2_shift9 (ZNF549)
; oligos_7nt_mkv5_m4 versus MA1728.2 (ZNF549); m=4/14; ncol2=8; w=0; offset=3; strand=D; shift=9; score=0.532689; ---------TGCTGCCC
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	0	483.0	72.0	50.0	229.0	28.0	55.0	106.0	183.0
c	0	0	0	0	0	0	0	0	0	349.0	161.0	4622.0	175.0	80.0	4364.0	4435.0	4133.0
g	0	0	0	0	0	0	0	0	0	498.0	4489.0	77.0	128.0	4566.0	177.0	98.0	75.0
t	0	0	0	0	0	0	0	0	0	3497.0	105.0	78.0	4295.0	153.0	231.0	188.0	436.0
MA1100.3_shift7 (ASCL1)
; oligos_7nt_mkv5_m4 versus MA1100.3 (ASCL1); m=5/14; ncol2=8; w=0; offset=1; strand=D; shift=7; score=0.520121; -------rCAGCTGc--
; cor=; Ncor=
a	0	0	0	0	0	0	0	1334.0	0.0	4413.0	107.0	729.0	118.0	52.0	177.0	0	0
c	0	0	0	0	0	0	0	521.0	4413.0	157.0	1288.0	4413.0	24.0	0.0	3065.0	0	0
g	0	0	0	0	0	0	0	3079.0	0.0	60.0	4413.0	1320.0	121.0	4413.0	814.0	0	0
t	0	0	0	0	0	0	0	354.0	14.0	218.0	625.0	20.0	4413.0	29.0	1349.0	0	0
MA1529.2_shift3 (NHLH2)
; oligos_7nt_mkv5_m4 versus MA1529.2 (NHLH2); m=6/14; ncol2=16; w=-3; offset=-3; strand=D; shift=3; score=0.48217; ---gGyMGCAGCTGCGy
; cor=; Ncor=
a	0	0	0	4312.0	3741.0	4921.0	5603.0	2378.0	2.0	21364.0	6.0	525.0	0.0	0.0	693.0	210.0	1184.0
c	0	0	0	2219.0	1065.0	6141.0	15451.0	2324.0	21359.0	0.0	2459.0	20268.0	14.0	2.0	20611.0	204.0	7207.0
g	0	0	0	13903.0	18450.0	4908.0	671.0	18930.0	2.0	26.0	20096.0	2266.0	3.0	21363.0	275.0	20977.0	1520.0
t	0	0	0	5198.0	2763.0	5394.0	151.0	2634.0	5.0	1.0	1054.0	0.0	21358.0	0.0	1230.0	740.0	13503.0
MA0697.3_rc_shift7 (Zic3_rc)
; oligos_7nt_mkv5_m4 versus MA0697.3_rc (Zic3_rc); m=7/14; ncol2=7; w=0; offset=1; strand=R; shift=7; score=0.46931; -------CCTGCTG---
; cor=; Ncor=
a	0	0	0	0	0	0	0	532.0	967.0	858.0	792.0	266.0	596.0	334.0	0	0	0
c	0	0	0	0	0	0	0	24340.0	24314.0	1768.0	756.0	24907.0	759.0	460.0	0	0	0
g	0	0	0	0	0	0	0	955.0	500.0	568.0	24272.0	670.0	872.0	25035.0	0	0	0
t	0	0	0	0	0	0	0	347.0	393.0	22980.0	354.0	331.0	23947.0	345.0	0	0	0
MA1628.2_rc_shift7 (Zic1::Zic2_rc)
; oligos_7nt_mkv5_m4 versus MA1628.2_rc (Zic1::Zic2_rc); m=8/14; ncol2=7; w=0; offset=1; strand=R; shift=7; score=0.466685; -------CCTGCTG---
; cor=; Ncor=
a	0	0	0	0	0	0	0	124.0	90.0	4.0	428.0	74.0	4.0	163.0	0	0	0
c	0	0	0	0	0	0	0	9631.0	9279.0	627.0	96.0	9527.0	266.0	106.0	0	0	0
g	0	0	0	0	0	0	0	91.0	512.0	311.0	9293.0	195.0	384.0	9594.0	0	0	0
t	0	0	0	0	0	0	0	46.0	11.0	8950.0	75.0	96.0	9238.0	29.0	0	0	0
MA1997.2_shift8 (Olig2)
; oligos_7nt_mkv5_m4 versus MA1997.2 (Olig2); m=9/14; ncol2=6; w=0; offset=2; strand=D; shift=8; score=0.417324; --------CAGCTG---
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	10.0	59733.0	14.0	41.0	0.0	50.0	0	0	0
c	0	0	0	0	0	0	0	0	60968.0	668.0	18.0	61069.0	741.0	114.0	0	0	0
g	0	0	0	0	0	0	0	0	114.0	741.0	61069.0	18.0	668.0	60968.0	0	0	0
t	0	0	0	0	0	0	0	0	50.0	0.0	41.0	14.0	59733.0	10.0	0	0	0
MA1938.2_rc_shift0 (ERF::NHLH1_rc)
; oligos_7nt_mkv5_m4 versus MA1938.2_rc (ERF::NHLH1_rc); m=10/14; ncol2=16; w=-6; offset=-6; strand=R; shift=0; score=0.416239; ryWTCCGGCAGCTGCt-
; cor=; Ncor=
a	210.0	40.0	84.0	12.0	26.0	7.0	1.0	8.0	15.0	324.0	8.0	28.0	0.0	18.0	21.0	7.0	0
c	16.0	176.0	11.0	3.0	313.0	325.0	11.0	6.0	317.0	13.0	2.0	288.0	0.0	14.0	290.0	81.0	0
g	108.0	3.0	0.0	21.0	10.0	0.0	327.0	316.0	12.0	20.0	301.0	11.0	0.0	317.0	14.0	81.0	0
t	0.0	113.0	241.0	324.0	4.0	27.0	12.0	0.0	1.0	10.0	26.0	1.0	324.0	5.0	0.0	156.0	0
MA1993.2_shift8 (Neurod2)
; oligos_7nt_mkv5_m4 versus MA1993.2 (Neurod2); m=11/14; ncol2=6; w=0; offset=2; strand=D; shift=8; score=  0.416; --------CAGCTG---
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	14.0	53280.0	8.0	17.0	0.0	39.0	0	0	0
c	0	0	0	0	0	0	0	0	53913.0	310.0	15.0	53984.0	434.0	58.0	0	0	0
g	0	0	0	0	0	0	0	0	58.0	434.0	53984.0	15.0	310.0	53913.0	0	0	0
t	0	0	0	0	0	0	0	0	39.0	0.0	17.0	8.0	53280.0	14.0	0	0	0
MA0633.3_shift8 (Twist2)
; oligos_7nt_mkv5_m4 versus MA0633.3 (Twist2); m=12/14; ncol2=6; w=0; offset=2; strand=D; shift=8; score=0.415902; --------CAGCTG---
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	15.0	48915.0	9.0	21.0	0.0	60.0	0	0	0
c	0	0	0	0	0	0	0	0	49473.0	345.0	16.0	49583.0	369.0	81.0	0	0	0
g	0	0	0	0	0	0	0	0	81.0	369.0	49583.0	16.0	342.0	49473.0	0	0	0
t	0	0	0	0	0	0	0	0	60.0	0.0	21.0	9.0	48918.0	15.0	0	0	0
MA1635.2_shift8 (BHLHE22)
; oligos_7nt_mkv5_m4 versus MA1635.2 (BHLHE22); m=13/14; ncol2=6; w=0; offset=2; strand=D; shift=8; score=0.414403; --------CAGCTG---
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	0.0	18267.0	1.0	14.0	0.0	14.0	0	0	0
c	0	0	0	0	0	0	0	0	18331.0	37.0	53.0	18288.0	52.0	15.0	0	0	0
g	0	0	0	0	0	0	0	0	11.0	52.0	18288.0	53.0	37.0	18327.0	0	0	0
t	0	0	0	0	0	0	0	0	14.0	0.0	14.0	1.0	18267.0	0.0	0	0	0
MA0521.3_shift8 (Tcf12)
; oligos_7nt_mkv5_m4 versus MA0521.3 (Tcf12); m=14/14; ncol2=6; w=0; offset=2; strand=D; shift=8; score=0.412347; --------CAGCTG---
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	367.0	72283.0	836.0	1565.0	341.0	549.0	0	0	0
c	0	0	0	0	0	0	0	0	72674.0	739.0	1814.0	69780.0	632.0	402.0	0	0	0
g	0	0	0	0	0	0	0	0	404.0	632.0	69780.0	1814.0	738.0	72670.0	0	0	0
t	0	0	0	0	0	0	0	0	550.0	341.0	1565.0	836.0	72284.0	374.0	0	0	0