One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203809_2026-03-30.203809_WvTw0s/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_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/2026/03/30/peak-motifs.2026-03-30.203809_2026-03-30.203809_WvTw0s/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift2 ; 16 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)    
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --mwAAGTGCTrr
; Alignment reference
a	0	0	60	81	182	186	8	6	10	13	14	61	62
c	0	0	56	36	6	8	4	4	3	191	2	28	37
g	0	0	44	27	6	6	197	1	187	2	2	79	62
t	0	0	52	68	18	12	3	201	12	6	194	44	51
MA0122.4_rc_shift2 (Nkx3-2_rc)
; oligos_7nt_mkv4_m5 versus MA0122.4_rc (Nkx3-2_rc); m=1/15; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.703344; --tTAAGTGktt-
; cor=; Ncor=
a	0	0	2241.0	325.0	9919.0	10109.0	94.0	212.0	218.0	1033.0	2359.0	2088.0	0
c	0	0	1368.0	68.0	68.0	29.0	10.0	19.0	23.0	1504.0	1154.0	1466.0	0
g	0	0	991.0	147.0	138.0	32.0	9965.0	82.0	9900.0	5079.0	1109.0	952.0	0
t	0	0	5620.0	9680.0	95.0	50.0	151.0	9907.0	79.0	2604.0	5598.0	5714.0	0
MA0495.4_rc_shift3 (MAFF_rc)
; oligos_7nt_mkv4_m5 versus MA0495.4_rc (MAFF_rc); m=2/15; ncol2=11; w=0; offset=1; strand=R; shift=3; score=0.628007; ---aAAaTGCTGA
; cor=; Ncor=
a	0	0	0	24063.0	28039.0	26745.0	21305.0	1690.0	694.0	2785.0	660.0	668.0	36393.0
c	0	0	0	2339.0	1498.0	1833.0	4442.0	1041.0	418.0	33923.0	444.0	330.0	409.0
g	0	0	0	4819.0	2423.0	2009.0	4360.0	559.0	36228.0	400.0	152.0	35020.0	369.0
t	0	0	0	6525.0	5786.0	7159.0	7639.0	34456.0	406.0	638.0	36490.0	1728.0	575.0
MA0672.2_rc_shift2 (NKX2-3_rc)
; oligos_7nt_mkv4_m5 versus MA0672.2_rc (NKX2-3_rc); m=3/15; ncol2=8; w=0; offset=0; strand=R; shift=2; score= 0.6116; --tyAAGTGs---
; cor=; Ncor=
a	0	0	2437.0	343.0	9278.0	9278.0	0.0	250.0	132.0	140.0	0	0	0
c	0	0	1831.0	5037.0	0.0	18.0	0.0	16.0	0.0	4499.0	0	0	0
g	0	0	917.0	1451.0	939.0	0.0	9278.0	98.0	9278.0	9278.0	0	0	0
t	0	0	9278.0	4241.0	0.0	0.0	8.0	9278.0	38.0	2025.0	0	0	0
MA2336.1_rc_shift5 (ZSCAN21_rc)
; oligos_7nt_mkv4_m5 versus MA2336.1_rc (ZSCAN21_rc); m=4/15; ncol2=7; w=0; offset=3; strand=R; shift=5; score=0.599243; -----AGTGCTT-
; cor=; Ncor=
a	0	0	0	0	0	885.0	11.0	11.0	154.0	41.0	10.0	65.0	0
c	0	0	0	0	0	16.0	30.0	22.0	32.0	853.0	25.0	55.0	0
g	0	0	0	0	0	9.0	881.0	21.0	744.0	25.0	16.0	124.0	0
t	0	0	0	0	0	37.0	25.0	893.0	17.0	28.0	896.0	703.0	0
MA0117.3_shift3 (Mafb)
; oligos_7nt_mkv4_m5 versus MA0117.3 (Mafb); m=5/15; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.597188; ---awwwTGCTGA
; cor=; Ncor=
a	0	0	0	1237.0	1263.0	1080.0	744.0	264.0	2.0	295.0	31.0	45.0	2182.0
c	0	0	0	174.0	121.0	216.0	398.0	618.0	14.0	2182.0	36.0	13.0	13.0
g	0	0	0	326.0	159.0	182.0	429.0	31.0	2182.0	5.0	2.0	2182.0	17.0
t	0	0	0	446.0	639.0	704.0	611.0	2182.0	5.0	7.0	2182.0	170.0	13.0
MA0673.2_rc_shift2 (NKX2-8_rc)
; oligos_7nt_mkv4_m5 versus MA0673.2_rc (NKX2-8_rc); m=6/15; ncol2=8; w=0; offset=0; strand=R; shift=2; score=0.595066; --TsRAGTGs---
; cor=; Ncor=
a	0	0	2158.0	271.0	8562.0	8562.0	110.0	516.0	2155.0	249.0	0	0	0
c	0	0	696.0	4286.0	0.0	0.0	0.0	0.0	0.0	2843.0	0	0	0
g	0	0	908.0	2267.0	3197.0	91.0	8562.0	595.0	8562.0	3529.0	0	0	0
t	0	0	8562.0	1738.0	23.0	0.0	14.0	8562.0	70.0	1942.0	0	0	0
MA0842.3_shift3 (NRL)
; oligos_7nt_mkv4_m5 versus MA0842.3 (NRL); m=7/15; ncol2=12; w=0; offset=1; strand=D; shift=3; score=0.573288; ---awwrTGCTGA
; cor=; Ncor=
a	0	0	0	21189.0	17467.0	14033.0	6835.0	581.0	1.0	1008.0	0.0	73.0	27228.0
c	0	0	0	838.0	319.0	1314.0	5669.0	2768.0	0.0	27228.0	8.0	0.0	0.0
g	0	0	0	3685.0	635.0	822.0	7983.0	68.0	27228.0	22.0	0.0	27228.0	4.0
t	0	0	0	6039.0	9761.0	13194.0	6741.0	27228.0	0.0	14.0	27228.0	1036.0	0.0
MA2003.2_rc_shift2 (NKX2-4_rc)
; oligos_7nt_mkv4_m5 versus MA2003.2_rc (NKX2-4_rc); m=8/15; ncol2=8; w=0; offset=0; strand=R; shift=2; score=0.553145; --TsAAGTGg---
; cor=; Ncor=
a	0	0	153.0	58.0	1185.0	1185.0	0.0	207.0	129.0	61.0	0	0	0
c	0	0	57.0	640.0	13.0	1.0	0.0	17.0	7.0	485.0	0	0	0
g	0	0	56.0	545.0	409.0	25.0	1185.0	127.0	1185.0	1185.0	0	0	0
t	0	0	1185.0	243.0	52.0	0.0	0.0	1185.0	14.0	385.0	0	0	0
MA0124.3_rc_shift3 (Nkx3-1_rc)
; oligos_7nt_mkv4_m5 versus MA0124.3_rc (Nkx3-1_rc); m=9/15; ncol2=7; w=0; offset=1; strand=R; shift=3; score=0.528172; ---TAAGTGg---
; cor=; Ncor=
a	0	0	0	523.0	5335.0	5335.0	9.0	88.0	336.0	275.0	0	0	0
c	0	0	0	173.0	0.0	0.0	9.0	10.0	10.0	1776.0	0	0	0
g	0	0	0	273.0	254.0	1.0	5335.0	28.0	5335.0	5335.0	0	0	0
t	0	0	0	5335.0	0.0	0.0	59.0	5335.0	0.0	981.0	0	0	0
MA1994.2_rc_shift2 (Nkx2-1_rc)
; oligos_7nt_mkv4_m5 versus MA1994.2_rc (Nkx2-1_rc); m=10/15; ncol2=7; w=0; offset=0; strand=R; shift=2; score=0.52705; --TCAAGTG----
; cor=; Ncor=
a	0	0	541.0	518.0	15157.0	15106.0	316.0	343.0	886.0	0	0	0	0
c	0	0	213.0	14172.0	315.0	605.0	118.0	146.0	181.0	0	0	0	0
g	0	0	243.0	657.0	518.0	162.0	15640.0	275.0	14886.0	0	0	0	0
t	0	0	15245.0	895.0	252.0	369.0	168.0	15478.0	289.0	0	0	0	0
MA0914.2_rc_shift3 (ISL2_rc)
; oligos_7nt_mkv4_m5 versus MA0914.2_rc (ISL2_rc); m=11/15; ncol2=6; w=0; offset=1; strand=R; shift=3; score=0.494436; ---TAAkTG----
; cor=; Ncor=
a	0	0	0	1354.0	5631.0	5631.0	398.0	248.0	1019.0	0	0	0	0
c	0	0	0	59.0	13.0	169.0	171.0	134.0	126.0	0	0	0	0
g	0	0	0	206.0	718.0	130.0	5631.0	162.0	5631.0	0	0	0	0
t	0	0	0	5631.0	278.0	218.0	3161.0	5631.0	160.0	0	0	0	0
MA0063.3_rc_shift2 (NKX2-5_rc)
; oligos_7nt_mkv4_m5 versus MA0063.3_rc (NKX2-5_rc); m=12/15; ncol2=7; w=0; offset=0; strand=R; shift=2; score=0.44759; --TTGAGTG----
; cor=; Ncor=
a	0	0	250.0	288.0	841.0	5166.0	153.0	74.0	322.0	0	0	0	0
c	0	0	98.0	217.0	62.0	61.0	49.0	76.0	24.0	0	0	0	0
g	0	0	165.0	120.0	4319.0	82.0	5098.0	48.0	5002.0	0	0	0	0
t	0	0	4931.0	4819.0	222.0	135.0	144.0	5246.0	96.0	0	0	0	0
MA1106.2_shift4 (HIF1A)
; oligos_7nt_mkv4_m5 versus MA1106.2 (HIF1A); m=13/15; ncol2=6; w=0; offset=2; strand=D; shift=4; score=0.415926; ----ACGTGC---
; cor=; Ncor=
a	0	0	0	0	976.0	0.0	1.0	2.0	84.0	88.0	0	0	0
c	0	0	0	0	0.0	979.0	0.0	33.0	41.0	837.0	0	0	0
g	0	0	0	0	2.0	0.0	979.0	11.0	844.0	20.0	0	0	0
t	0	0	0	0	2.0	1.0	0.0	934.0	11.0	35.0	0	0	0
MA2329.1_rc_shift0 (ZBTB11_rc)
; oligos_7nt_mkv4_m5 versus MA2329.1_rc (ZBTB11_rc); m=14/15; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.402726; CCGGAAGTG----
; cor=; Ncor=
a	91.0	319.0	27.0	9.0	2293.0	2176.0	106.0	78.0	153.0	0	0	0	0
c	2030.0	1977.0	25.0	15.0	31.0	101.0	84.0	262.0	188.0	0	0	0	0
g	230.0	74.0	2328.0	2342.0	33.0	39.0	2192.0	120.0	1926.0	0	0	0	0
t	44.0	25.0	15.0	29.0	38.0	79.0	13.0	1935.0	128.0	0	0	0	0
MA0473.4_shift0 (ELF1)
; oligos_7nt_mkv4_m5 versus MA0473.4 (ELF1); m=15/15; ncol2=9; w=-2; offset=-2; strand=D; shift=0; score=0.401912; CAGGAAGTG----
; cor=; Ncor=
a	3094.0	42164.0	320.0	649.0	45930.0	45243.0	4063.0	3009.0	5688.0	0	0	0	0
c	37923.0	4038.0	421.0	505.0	796.0	705.0	1570.0	1993.0	4236.0	0	0	0	0
g	4819.0	932.0	46642.0	45970.0	676.0	779.0	41738.0	2007.0	34757.0	0	0	0	0
t	1934.0	636.0	387.0	646.0	368.0	1043.0	399.0	40761.0	3089.0	0	0	0	0