One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/04/peak-motifs.2026-03-04.105925_2026-03-04.105925_GBNx32/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.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/2026/03/04/peak-motifs.2026-03-04.105925_2026-03-04.105925_GBNx32/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 12 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)    
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; yhcaTTTGCATaAcAAwgsmm
; Alignment reference
a	141	209	180	501	47	82	96	99	42	766	25	519	544	55	658	688	459	195	178	270	218
c	223	205	311	89	38	104	22	40	726	12	29	59	32	501	49	31	39	58	219	216	233
g	189	146	126	96	24	45	8	633	9	5	13	123	28	148	24	43	42	485	306	181	169
t	237	230	173	104	681	559	664	18	13	7	723	89	186	86	59	28	250	52	87	123	170
MA1962.1_shift2 (POU2F1::SOX2)
; oligos_6nt_mkv3_m3 versus MA1962.1 (POU2F1::SOX2); m=1/11; ncol2=17; w=0; offset=2; strand=D; shift=2; score=0.754789; --mATTWrCATmACAAWrg--
; cor=; Ncor=
a	0	0	7886.0	15701.0	553.0	1136.0	5710.0	5841.0	1656.0	15595.0	32.0	7899.0	16152.0	376.0	16231.0	16210.0	5996.0	7139.0	2147.0	0	0
c	0	0	4993.0	528.0	216.0	552.0	471.0	812.0	15582.0	113.0	154.0	5483.0	518.0	15839.0	175.0	133.0	340.0	636.0	3768.0	0	0
g	0	0	2541.0	434.0	22.0	53.0	65.0	10408.0	70.0	501.0	49.0	2557.0	158.0	683.0	89.0	61.0	87.0	7984.0	8916.0	0	0
t	0	0	825.0	1325.0	16133.0	16109.0	14381.0	25.0	141.0	35.0	16010.0	306.0	629.0	2079.0	372.0	127.0	13866.0	1558.0	1414.0	0	0
MA0142.1_rc_shift3 (Pou5f1::Sox2_rc)
; oligos_6nt_mkv3_m3 versus MA0142.1_rc (Pou5f1::Sox2_rc); m=2/11; ncol2=15; w=0; offset=3; strand=R; shift=3; score=0.705446; ---aTtTGCATrwsAAwr---
; cor=; Ncor=
a	0	0	0	837.0	53.0	92.0	269.0	196.0	104.0	1332.0	80.0	612.0	907.0	63.0	1231.0	1270.0	701.0	389.0	0	0	0
c	0	0	0	207.0	75.0	315.0	30.0	129.0	1239.0	15.0	24.0	186.0	29.0	825.0	79.0	36.0	28.0	66.0	0	0	0
g	0	0	0	119.0	33.0	68.0	16.0	1029.0	16.0	5.0	30.0	365.0	18.0	363.0	12.0	50.0	58.0	846.0	0	0	0
t	0	0	0	198.0	1200.0	887.0	1050.0	14.0	10.0	17.0	1235.0	206.0	415.0	118.0	47.0	11.0	579.0	63.0	0	0	0
MA0507.3_rc_shift0 (POU2F2_rc)
; oligos_6nt_mkv3_m3 versus MA0507.3_rc (POU2F2_rc); m=3/11; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.566316; cTmATTTGCATAw--------
; cor=; Ncor=
a	788.0	1065.0	5505.0	9207.0	8.0	57.0	1929.0	1193.0	111.0	9207.0	0.0	9207.0	3315.0	0	0	0	0	0	0	0	0
c	5392.0	851.0	3703.0	35.0	0.0	23.0	0.0	127.0	9207.0	2.0	0.0	4.0	2020.0	0	0	0	0	0	0	0	0
g	1301.0	648.0	862.0	8.0	5.0	7.0	0.0	8014.0	0.0	13.0	0.0	100.0	435.0	0	0	0	0	0	0	0	0
t	1726.0	6644.0	1399.0	56.0	9207.0	9207.0	7279.0	2.0	0.0	0.0	9207.0	34.0	5892.0	0	0	0	0	0	0	0	0
MA0784.3_shift0 (POU1F1)
; oligos_6nt_mkv3_m3 versus MA0784.3 (POU1F1); m=4/11; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.56559; CTmATTwGCATAwt-------
; cor=; Ncor=
a	131.0	106.0	2281.0	4127.0	0.0	91.0	1564.0	419.0	54.0	4127.0	3.0	4127.0	2323.0	849.0	0	0	0	0	0	0	0
c	3623.0	126.0	1846.0	7.0	0.0	13.0	0.0	67.0	4127.0	9.0	3.0	5.0	165.0	702.0	0	0	0	0	0	0	0
g	372.0	220.0	192.0	28.0	1.0	2.0	0.0	3708.0	1.0	5.0	0.0	5.0	57.0	384.0	0	0	0	0	0	0	0
t	504.0	3907.0	262.0	31.0	4127.0	4127.0	2563.0	16.0	3.0	17.0	4127.0	59.0	1804.0	3278.0	0	0	0	0	0	0	0
MA0788.1_rc_shift1 (POU3F3_rc)
; oligos_6nt_mkv3_m3 versus MA0788.1_rc (POU3F3_rc); m=5/11; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.530106; -waATTwGCATAww-------
; cor=; Ncor=
a	0	542.0	1078.0	1078.0	14.0	79.0	572.0	343.0	86.0	1078.0	30.0	1078.0	637.0	290.0	0	0	0	0	0	0	0
c	0	115.0	237.0	12.0	15.0	77.0	1.0	118.0	1078.0	49.0	12.0	64.0	131.0	137.0	0	0	0	0	0	0	0
g	0	85.0	141.0	20.0	6.0	11.0	4.0	1078.0	10.0	33.0	11.0	57.0	41.0	75.0	0	0	0	0	0	0	0
t	0	536.0	240.0	53.0	1078.0	1078.0	506.0	28.0	22.0	25.0	1078.0	129.0	440.0	576.0	0	0	0	0	0	0	0
MA0787.1_rc_shift1 (POU3F2_rc)
; oligos_6nt_mkv3_m3 versus MA0787.1_rc (POU3F2_rc); m=6/11; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.527342; -tmATTwGCATAw--------
; cor=; Ncor=
a	0	562.0	840.0	1292.0	13.0	45.0	604.0	372.0	60.0	1292.0	0.0	1292.0	700.0	0	0	0	0	0	0	0	0
c	0	261.0	452.0	28.0	0.0	32.0	1.0	153.0	1292.0	12.0	25.0	40.0	171.0	0	0	0	0	0	0	0	0
g	0	262.0	165.0	19.0	6.0	16.0	4.0	1292.0	9.0	30.0	16.0	65.0	61.0	0	0	0	0	0	0	0	0
t	0	1292.0	137.0	63.0	1292.0	1292.0	688.0	68.0	19.0	28.0	1292.0	163.0	591.0	0	0	0	0	0	0	0	0
MA0786.2_rc_shift3 (POU3F1_rc)
; oligos_6nt_mkv3_m3 versus MA0786.2_rc (POU3F1_rc); m=7/11; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.453924; ---ATTwrCATAw--------
; cor=; Ncor=
a	0	0	0	2471.0	63.0	284.0	1048.0	1119.0	232.0	2471.0	21.0	2471.0	1437.0	0	0	0	0	0	0	0	0
c	0	0	0	128.0	25.0	130.0	21.0	413.0	2471.0	21.0	26.0	128.0	322.0	0	0	0	0	0	0	0	0
g	0	0	0	95.0	20.0	103.0	1.0	2471.0	13.0	53.0	7.0	186.0	126.0	0	0	0	0	0	0	0	0
t	0	0	0	259.0	2471.0	2471.0	1423.0	170.0	37.0	44.0	2471.0	505.0	1034.0	0	0	0	0	0	0	0	0
MA0627.3_rc_shift3 (POU2F3_rc)
; oligos_6nt_mkv3_m3 versus MA0627.3_rc (POU2F3_rc); m=8/11; ncol2=9; w=0; offset=3; strand=R; shift=3; score=0.424627; ---ATTTGCATa---------
; cor=; Ncor=
a	0	0	0	43338.0	330.0	3276.0	896.0	3716.0	2827.0	53366.0	931.0	37593.0	0	0	0	0	0	0	0	0	0
c	0	0	0	4098.0	233.0	804.0	138.0	1079.0	51971.0	1251.0	354.0	3029.0	0	0	0	0	0	0	0	0	0
g	0	0	0	3478.0	164.0	567.0	80.0	50288.0	251.0	322.0	194.0	6885.0	0	0	0	0	0	0	0	0	0
t	0	0	0	5115.0	55302.0	51382.0	54915.0	946.0	980.0	1090.0	54550.0	8522.0	0	0	0	0	0	0	0	0	0
MA0785.2_rc_shift3 (POU2F1_rc)
; oligos_6nt_mkv3_m3 versus MA0785.2_rc (POU2F1_rc); m=9/11; ncol2=9; w=0; offset=3; strand=R; shift=3; score=0.416793; ---ATTwgCATA---------
; cor=; Ncor=
a	0	0	0	10582.0	158.0	787.0	3651.0	3375.0	1326.0	10582.0	43.0	10582.0	0	0	0	0	0	0	0	0	0
c	0	0	0	755.0	51.0	879.0	46.0	1351.0	10582.0	213.0	29.0	474.0	0	0	0	0	0	0	0	0	0
g	0	0	0	457.0	37.0	108.0	33.0	10582.0	82.0	501.0	12.0	1347.0	0	0	0	0	0	0	0	0	0
t	0	0	0	1422.0	10582.0	10582.0	6932.0	300.0	186.0	153.0	10582.0	756.0	0	0	0	0	0	0	0	0	0
MA0792.1_rc_shift3 (POU5F1B_rc)
; oligos_6nt_mkv3_m3 versus MA0792.1_rc (POU5F1B_rc); m=10/11; ncol2=9; w=0; offset=3; strand=R; shift=3; score=0.416653; ---ATTwrCATA---------
; cor=; Ncor=
a	0	0	0	9519.0	203.0	896.0	3220.0	3828.0	1790.0	9519.0	84.0	9519.0	0	0	0	0	0	0	0	0	0
c	0	0	0	750.0	97.0	856.0	65.0	1293.0	9519.0	206.0	67.0	808.0	0	0	0	0	0	0	0	0	0
g	0	0	0	537.0	65.0	144.0	51.0	9519.0	94.0	364.0	21.0	1778.0	0	0	0	0	0	0	0	0	0
t	0	0	0	1559.0	9519.0	9519.0	6299.0	398.0	322.0	171.0	9519.0	1326.0	0	0	0	0	0	0	0	0	0
MA0789.1_rc_shift3 (POU3F4_rc)
; oligos_6nt_mkv3_m3 versus MA0789.1_rc (POU3F4_rc); m=11/11; ncol2=9; w=0; offset=3; strand=R; shift=3; score=0.412927; ---ATTwGCATA---------
; cor=; Ncor=
a	0	0	0	11117.0	168.0	885.0	4670.0	2565.0	245.0	11117.0	26.0	11117.0	0	0	0	0	0	0	0	0	0
c	0	0	0	292.0	88.0	315.0	56.0	602.0	11117.0	24.0	68.0	136.0	0	0	0	0	0	0	0	0	0
g	0	0	0	247.0	47.0	332.0	10.0	11117.0	19.0	59.0	23.0	349.0	0	0	0	0	0	0	0	0	0
t	0	0	0	705.0	11117.0	11117.0	6447.0	136.0	53.0	59.0	11117.0	941.0	0	0	0	0	0	0	0	0	0