Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005643.1 Hibiscus syriacus cultivar Beakdansim tig00013156_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42359
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:804 original size:23 final size:24
Alignment explanation
Indices: 771--823 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
761 CTGAAACATC
*
771 ATCAAAATCCGAGTA-TGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
794 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
818 ATCAAA
1 ATCAAA
824 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1870 original size:19 final size:20
Alignment explanation
Indices: 1812--1881 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
1802 ATTCATTTGA
1812 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1832 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1852 CTATCGCAATGTG-AAATGG
1 CTATCGCAACGCGAAAATGG
1871 CTATCGCAACG
1 CTATCGCAACG
1882 ACAAAATCGC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 16 0.34
20 31 0.66
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1948 original size:19 final size:19
Alignment explanation
Indices: 1907--1971 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
1897 GAAATGAAAA
1907 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1923 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1940 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1959 TCGCATTGCGATT
1 TCGCATTGCGATT
1972 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2002 original size:20 final size:20
Alignment explanation
Indices: 1977--2015 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1967 CGATTCTCTC
1977 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
1997 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
2016 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:2117 original size:14 final size:14
Alignment explanation
Indices: 2098--2134 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2088 CATCAATTAA
2098 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2112 ACAAATCATCTTTT
1 ACAAATCAACATTT
2126 ACAAATCAA
1 ACAAATCAA
2135 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:4007 original size:20 final size:20
Alignment explanation
Indices: 3982--4027 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3972 TAGTTTACTT
3982 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
4002 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
4022 TCGCAA
1 TCGCAA
4028 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:4036 original size:19 final size:20
Alignment explanation
Indices: 3993--4037 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3983 CGCAACACGA
3993 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
4013 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
4032 AAATGA
1 AAATGA
4038 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:4043 original size:19 final size:19
Alignment explanation
Indices: 4001--4116 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
3991 GAAAATGACT
***
4001 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
4021 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4040 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
4054 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
* *
4072 ACCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
4086 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4105 ATCGCAATGCGA
1 ATCGCAATGCGA
4117 TTTGTGTTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
14 19 0.25
15 1 0.01
16 6 0.08
17 2 0.03
18 10 0.13
19 27 0.36
20 10 0.13
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4056 original size:14 final size:14
Alignment explanation
Indices: 4037--4094 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
4027 ATGCGAAATG
4037 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4051 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
4067 ATGAAACCGCAACGAC
1 A--AAATCGCAACGAC
4083 AAAATCGCAACG
1 AAAATCGCAACG
4095 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4063 original size:33 final size:33
Alignment explanation
Indices: 4021--4111 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
4011 GGAAATGGCT
4021 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
4054 ATCGCAATGCGAAATG-AAACCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
4086 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
4112 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:4145 original size:14 final size:14
Alignment explanation
Indices: 4123--4185 Score: 56
Period size: 14 Copynumber: 4.3 Consensus size: 14
4113 GCGATTTGTG
4123 TTTTG-CGTTGCGA
1 TTTTGTCGTTGCGA
**
4136 TTTTGTCGTTGTAA
1 TTTTGTCGTTGCGA
*
4150 TTTCATTTCGCATTGCGA
1 TTT--TGTCG--TTGCGA
4168 TTTTGTCGTTGCGA
1 TTTTGTCGTTGCGA
4182 TTTT
1 TTTT
4186 CATTTCGCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
13 5 0.13
14 19 0.49
16 8 0.21
18 7 0.18
ACGTcount: A:0.11, C:0.14, G:0.22, T:0.52
Consensus pattern (14 bp):
TTTTGTCGTTGCGA
Found at i:4171 original size:32 final size:33
Alignment explanation
Indices: 4130--4201 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
4120 GTGTTTTGCG
*
4130 TTGCGATTTTGTCGTTG-TAATTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGAATTTCATTTCGCA
*
4162 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGAATTTCATTTCGCA
4195 TTGCGAT
1 TTGCGAT
4202 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
32 17 0.46
33 20 0.54
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGAATTTCATTTCGCA
Found at i:4200 original size:19 final size:19
Alignment explanation
Indices: 4150--4221 Score: 64
Period size: 19 Copynumber: 4.0 Consensus size: 19
4140 GTCGTTGTAA
4150 TTTCATTTCGCATTGCGA-
1 TTTCATTTCGCATTGCGAT
*
4168 TTT--TGTCG--TTGCGAT
1 TTTCATTTCGCATTGCGAT
4183 TTTCATTTCGCATTGCGAT
1 TTTCATTTCGCATTGCGAT
***
4202 AGCCATTTCCGCATTGCGAT
1 TTTCATTT-CGCATTGCGAT
4222 AGTCATTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.14
15 3 0.07
16 4 0.09
17 4 0.09
18 3 0.07
19 12 0.28
20 11 0.26
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
TTTCATTTCGCATTGCGAT
Found at i:4240 original size:20 final size:20
Alignment explanation
Indices: 4186--4229 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
4176 TTGCGATTTT
4186 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
4205 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
4225 CATTT
1 CATTT
4230 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:4748 original size:18 final size:18
Alignment explanation
Indices: 4722--4766 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4712 GTCGATCAGA
*
4722 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
4740 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
4758 TGATGGCTC
1 TGATGGCTC
4767 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:6132 original size:20 final size:20
Alignment explanation
Indices: 6084--6142 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
6074 AATAGTTTCT
** *
6084 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
6104 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
6124 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
6143 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:6430 original size:22 final size:21
Alignment explanation
Indices: 6396--6444 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
6386 TCTGAGAGAT
6396 GGAGAT-AGACGGATTTCGTC
1 GGAGATGAGACGGATTTCGTC
6416 GGAGATGAGGACGGATTTCGTC
1 GGAGATGA-GACGGATTTCGTC
6438 GGAGATG
1 GGAGATG
6445 GGTGAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.22
21 1 0.04
22 20 0.74
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.22
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGTC
Found at i:6720 original size:61 final size:61
Alignment explanation
Indices: 6614--6751 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
6604 CGCTTTGAAA
* * * *
6614 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
6675 ATCTCGTTGCGATTTTGTATTATTGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
6736 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
6752 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:6724 original size:20 final size:20
Alignment explanation
Indices: 6614--6748 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
6604 CGCTTTGAAA
*
6614 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
6635 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
6655 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
6675 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
* *
6696 ATTGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
6716 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
6736 ATCGCATTGCGAT
1 ATCGCATTGCGAT
6749 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 65 0.69
21 22 0.23
22 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:7769 original size:19 final size:19
Alignment explanation
Indices: 7736--7772 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7726 ATGACCAACA
**
7736 AAATCGCAATGCGATCTCT
1 AAATCGCAACACGATCTCT
7755 AAATCGCAACACGATCTC
1 AAATCGCAACACGATCTC
7773 CAGTATCGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACACGATCTCT
Found at i:8759 original size:24 final size:24
Alignment explanation
Indices: 8727--8780 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
8717 GTATTCAAAA
8727 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
8751 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
8775 TTTGAT
1 TTTGAT
8781 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:11069 original size:18 final size:18
Alignment explanation
Indices: 11046--11080 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11036 AGAAAAAGGC
*
11046 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
11064 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
11081 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:11406 original size:20 final size:20
Alignment explanation
Indices: 11381--11537 Score: 206
Period size: 20 Copynumber: 7.8 Consensus size: 20
11371 TTACACATTC
* *
11381 ATTTGAATATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
11401 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
11421 ATTTGACTATTGCAATGTGA
1 ATTTGACTATCGCAACGCGA
*
11441 ATTTAACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
11461 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
***
11481 ATTTGACTATCGCAATATGA
1 ATTTGACTATCGCAACGCGA
* *
11501 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
11521 AGTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
11538 AGAAAATCAC
Statistics
Matches: 118, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 118 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:11465 original size:60 final size:60
Alignment explanation
Indices: 11392--11537 Score: 238
Period size: 60 Copynumber: 2.4 Consensus size: 60
11382 TTTGAATATT
* *
11392 GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATTGCAATGTGAATTTAACTATC
1 GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAATATGAATTTAACTATC
* *
11452 GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAATATGAATTTGATTATC
1 GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAATATGAATTTAACTATC
* *
11512 GCAACGGGAAGTTGACTATCGCAACG
1 GCAACGCGAATTTGACTATCGCAACG
11538 AGAAAATCAC
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (60 bp):
GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAATATGAATTTAACTATC
Found at i:11605 original size:20 final size:20
Alignment explanation
Indices: 11576--11653 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
11566 GCAACGCGAA
* *
11576 TTGACTTTCGCGTTGTGATT
1 TTGACTTTCGCATTGCGATT
*
11596 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
11616 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
11636 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
11654 AAGTGTACCT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:11788 original size:27 final size:28
Alignment explanation
Indices: 11756--11809 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
11746 AATAAGAATT
*
11756 ATTTACACATCAA-TTAAACAAATCAAC
1 ATTTACAAATCAACTTAAACAAATCAAC
**
11783 ATTTACAAATCAACTTTTACAAATCAA
1 ATTTACAAATCAACTTAAACAAATCAA
11810 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (28 bp):
ATTTACAAATCAACTTAAACAAATCAAC
Found at i:11792 original size:14 final size:14
Alignment explanation
Indices: 11773--11809 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
11763 CATCAATTAA
11773 ACAAATCAACATTT
1 ACAAATCAACATTT
*
11787 ACAAATCAACTTTT
1 ACAAATCAACATTT
11801 ACAAATCAA
1 ACAAATCAA
11810 TTAAACAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:13155 original size:21 final size:21
Alignment explanation
Indices: 13095--13212 Score: 92
Period size: 21 Copynumber: 5.6 Consensus size: 21
13085 GTGAATCGGG
* * * *
13095 CTCTTGAATGGTGGGAGAGAC
1 CTCTTGAACGATGGGAGGGGC
* * **
13116 CTCTTCAACAATGACAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
13137 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGGGAGGGGC
** **
13158 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* * *
13179 CTCTTGAATGATAGGAGAGGC
1 CTCTTGAACGATGGGAGGGGC
13200 CTCTTGAACGATG
1 CTCTTGAACGATG
13213 ACAGGTGAGT
Statistics
Matches: 71, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:13162 original size:42 final size:42
Alignment explanation
Indices: 13108--13217 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
13098 TTGAATGGTG
* * *
13108 GGAGA-GACCTCTTCAACAATGACAGGGGCCTCTTGAACGATG
1 GGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATA
* ** * *
13150 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAATGATA
1 GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
*
13192 GGAGAGGCCTCTTGAACGATGACAGG
1 GGAGAGGACTCTTGAACGATGACAGG
13218 TGAGTCGGGC
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 52 0.96
43 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.20
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
Found at i:13801 original size:19 final size:19
Alignment explanation
Indices: 13777--13840 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
13767 GCAACAAGAT
* * *
13777 AATCGCAATGTGAAATAAA
1 AATCGCAACGCGAAACAAA
*
13796 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
* *
13815 AATCGCAACGCCAAACTAA
1 AATCGCAACGCGAAACAAA
*
13834 ATTCGCA
1 AATCGCA
13841 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.47, C:0.25, G:0.14, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:13900 original size:20 final size:20
Alignment explanation
Indices: 13860--13926 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
13850 TTATTTCACA
**
13860 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCG
* *
13880 TTACGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCG
*
13900 TTGCGGTAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
13920 TTGCGAT
1 TTGCGAT
13927 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:15868 original size:20 final size:20
Alignment explanation
Indices: 15845--15934 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
15835 TCTGAAACTT
15845 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
15865 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
15885 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
15905 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
15924 AAAATCTCAAC
1 AAAATCGCAAC
15935 GAGAAAATCG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 11 0.18
20 49 0.82
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:16369 original size:22 final size:22
Alignment explanation
Indices: 16342--16389 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
16332 GGAGATAGAT
* *
16342 GGATTTCGCCGGAGATGGGGGC
1 GGATTTCGCCAGAGATGGGGAC
*
16364 GGATTTCGTCAGAGATGGGGAC
1 GGATTTCGCCAGAGATGGGGAC
16386 GGAT
1 GGAT
16390 GTCGTCGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.46, T:0.21
Consensus pattern (22 bp):
GGATTTCGCCAGAGATGGGGAC
Found at i:16394 original size:22 final size:22
Alignment explanation
Indices: 16353--16395 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16343 GATTTCGCCG
* *
16353 GAGATGGGGGCGGATTTCGTCA
1 GAGATGGGGACGGATGTCGTCA
16375 GAGATGGGGACGGATGTCGTC
1 GAGATGGGGACGGATGTCGTC
16396 GTAGAGAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.47, T:0.21
Consensus pattern (22 bp):
GAGATGGGGACGGATGTCGTCA
Found at i:16605 original size:20 final size:19
Alignment explanation
Indices: 16582--16627 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
16572 GGAAACTGAT
* *
16582 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
16602 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
16621 TTGCGAT
1 TTGCGAT
16628 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:16617 original size:19 final size:19
Alignment explanation
Indices: 16593--16629 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16583 TGCGATACTG
*
16593 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
16612 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
16630 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:17125 original size:18 final size:18
Alignment explanation
Indices: 17102--17137 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17092 CATCGTGTGA
17102 GCGTGAGGAGTTCCGACG
1 GCGTGAGGAGTTCCGACG
*
17120 GCGTGAGGAGTTCTGACG
1 GCGTGAGGAGTTCCGACG
17138 TCCATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.44, T:0.19
Consensus pattern (18 bp):
GCGTGAGGAGTTCCGACG
Found at i:17976 original size:29 final size:30
Alignment explanation
Indices: 17927--17984 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
17917 ATTTTGACTA
* *
17927 GTGACTAAAATGTAAATTTTG-AAAGTTTT
1 GTGACTAAAATGCAAACTTTGAAAAGTTTT
*
17956 GTGACTAAAGTGCAAACTTTGAAAAGTTT
1 GTGACTAAAATGCAAACTTTGAAAAGTTT
17985 AGCCAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (30 bp):
GTGACTAAAATGCAAACTTTGAAAAGTTTT
Found at i:29172 original size:3 final size:3
Alignment explanation
Indices: 29166--29267 Score: 177
Period size: 3 Copynumber: 34.0 Consensus size: 3
29156 AATATTTTTT
* * *
29166 TTA TTA TTA TTA TTA TTA TTA TCA TTA TCA TTA TTA TTA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29214 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29262 TTA TTA
1 TTA TTA
29268 AATATATTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:29733 original size:22 final size:22
Alignment explanation
Indices: 29690--29734 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
29680 ACAGAGACAG
* * * *
29690 AGACAGAGAACGGAGAAGAAAA
1 AGACAGAGAAAGAAAAAAAAAA
29712 AGACAGAGAAAGAAAAAAAAAA
1 AGACAGAGAAAGAAAAAAAAAA
29734 A
1 A
29735 ATAAACTAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.07, G:0.24, T:0.00
Consensus pattern (22 bp):
AGACAGAGAAAGAAAAAAAAAA
Found at i:30633 original size:20 final size:22
Alignment explanation
Indices: 30594--30635 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
30584 GATATTTTTA
*
30594 TTTTATTATATTGTATAAATAT
1 TTTTATTATATTGCATAAATAT
30616 TTTTA-TATATT-CATAAATAT
1 TTTTATTATATTGCATAAATAT
30636 ACTTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTATTATATTGCATAAATAT
Found at i:41945 original size:16 final size:15
Alignment explanation
Indices: 41921--41989 Score: 65
Period size: 14 Copynumber: 4.8 Consensus size: 15
41911 ATTATGCTTG
*
41921 AAAA-AAAAAAGAAG
1 AAAAGAAAAAAGAAA
* *
41935 AAAAGAAAAAAGGGAG
1 AAAAGAAAAAA-GAAA
*
41951 AAAAGAAAAGA-AAA
1 AAAAGAAAAAAGAAA
41965 AAAAGAAAAAAG--A
1 AAAAGAAAAAAGAAA
41978 AAAAGAAAAAAG
1 AAAAGAAAAAAG
41990 GATTAAGGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
13 13 0.28
14 15 0.32
15 6 0.13
16 13 0.28
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAGAAA
Found at i:41956 original size:21 final size:21
Alignment explanation
Indices: 41927--41990 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
41917 CTTGAAAAAA
41927 AAAAGAAGAAAAGAAAAAAGGG
1 AAAA-AAGAAAAGAAAAAAGGG
* **
41949 AGAAAAGAAAAGAAAAAAAAG
1 AAAAAAGAAAAGAAAAAAGGG
41970 AAAAAAGAAAAAGAAAAAAGG
1 AAAAAAG-AAAAGAAAAAAGG
41991 ATTAAGGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAGAAAAAAGGG
Done.