Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012496.1 Corchorus olitorius cultivar O-4 contig12529, 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: 9585
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:4088 original size:36 final size:36
Alignment explanation
Indices: 4048--4174 Score: 193
Period size: 36 Copynumber: 3.5 Consensus size: 36
4038 TTGCGCCCTA
* *
4048 CTCCTAGGGAGGAAGAAGTGAGGCGCACCCTATTAT
1 CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
4084 CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
1 CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
*
4120 C-CCTGGGGGAGGAAGAAGTAAGGCGCACCCTACTAT
1 CTCCT-GGGGAGGAAGAAGTAAGGCGCACCCTATTAT
* *
4156 CCCCTGGAGAGGAAGAAGT
1 CTCCTGGGGAGGAAGAAGT
4175 GTGACGCACC
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
35 3 0.04
36 79 0.93
37 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.32, T:0.17
Consensus pattern (36 bp):
CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
Found at i:4183 original size:36 final size:36
Alignment explanation
Indices: 4054--4188 Score: 182
Period size: 36 Copynumber: 3.8 Consensus size: 36
4044 CCTACTCCTA
* * *
4054 GGGAGGAAGAAGTGAGGCGCACCCTATTATCTCCTG
1 GGGAGGAAGAAGTAAGGCGCACCCTACTATCCCCTG
*
4090 GGGAGGAAGAAGTAAGGCGCACCCTATTAT-CCCTGG
1 GGGAGGAAGAAGTAAGGCGCACCCTACTATCCCCT-G
4126 GGGAGGAAGAAGTAAGGCGCACCCTACTATCCCCTG
1 GGGAGGAAGAAGTAAGGCGCACCCTACTATCCCCTG
* ** *
4162 GAGAGGAAGAAGTGTGACGCACCCTAC
1 GGGAGGAAGAAGTAAGGCGCACCCTAC
4189 CACGCTTAAG
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
35 3 0.03
36 83 0.92
37 4 0.04
ACGTcount: A:0.28, C:0.24, G:0.33, T:0.16
Consensus pattern (36 bp):
GGGAGGAAGAAGTAAGGCGCACCCTACTATCCCCTG
Found at i:6667 original size:54 final size:56
Alignment explanation
Indices: 6596--6720 Score: 191
Period size: 54 Copynumber: 2.2 Consensus size: 56
6586 CCAAGCGCAA
* * *
6596 GGGGGCTACCCCTTTGCTAGTAAAAAGGGGGATGA-CCCCCTGCCATGCGCAAA-G
1 GGGGGCGACCCCCTTGCTAGCAAAAAGGGGGATGACCCCCCTGCCATGCGCAAAGG
*
6650 GGGGGCGACCCCCTTGCTAGCAAAAAGGGGGATGACCCCCCTGCCATGCTCAAAGGG
1 GGGGGCGACCCCCTTGCTAGCAAAAAGGGGGATGACCCCCCTGCCATGCGCAAA-GG
6707 GGGGGCGACCCCCT
1 GGGGGCGACCCCCT
6721 GCCATGCGCA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
54 32 0.50
55 17 0.27
57 15 0.23
ACGTcount: A:0.22, C:0.31, G:0.34, T:0.14
Consensus pattern (56 bp):
GGGGGCGACCCCCTTGCTAGCAAAAAGGGGGATGACCCCCCTGCCATGCGCAAAGG
Found at i:6689 original size:27 final size:27
Alignment explanation
Indices: 6594--6689 Score: 97
Period size: 27 Copynumber: 3.6 Consensus size: 27
6584 AACCAAGCGC
* * *
6594 AAGGGGGCT-ACCCCTTTGCTAGTAAA
1 AAGGGGGATGACCCCCTTGCTAGCAAA
* **
6620 AAGGGGGATGACCCCC-TGCCATGCGCA
1 AAGGGGGATGACCCCCTTGCTA-GCAAA
**
6647 AAGGGGGGCGACCCCCTTGCTAGCAAA
1 AAGGGGGATGACCCCCTTGCTAGCAAA
6674 AAGGGGGATGACCCCC
1 AAGGGGGATGACCCCC
6690 CTGCCATGCT
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
26 12 0.22
27 38 0.70
28 4 0.07
ACGTcount: A:0.25, C:0.29, G:0.32, T:0.14
Consensus pattern (27 bp):
AAGGGGGATGACCCCCTTGCTAGCAAA
Found at i:6707 original size:27 final size:28
Alignment explanation
Indices: 6619--6708 Score: 103
Period size: 27 Copynumber: 3.3 Consensus size: 28
6609 TTGCTAGTAA
*
6619 AAAGGGGGATGA-CCCCCTGCCATGCGC
1 AAAGGGGGATGACCCCCCTGCCATGCAC
** * * *
6646 AAAGGGGGGCGACCCCCTTGCTA-GCAA
1 AAAGGGGGATGACCCCCCTGCCATGCAC
*
6673 AAAGGGGGATGACCCCCCTGCCATGCTC
1 AAAGGGGGATGACCCCCCTGCCATGCAC
6701 AAAGGGGG
1 AAAGGGGG
6709 GGGCGACCCC
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
27 31 0.63
28 18 0.37
ACGTcount: A:0.24, C:0.30, G:0.34, T:0.11
Consensus pattern (28 bp):
AAAGGGGGATGACCCCCCTGCCATGCAC
Found at i:6816 original size:14 final size:14
Alignment explanation
Indices: 6792--6839 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
6782 GCTAAAAAAA
6792 AATAACAAAAATAAT
1 AATAAC-AAAATAAT
* *
6807 AATAATAAAAAAAT
1 AATAACAAAATAAT
6821 AATAACAACAATAA-
1 AATAACAA-AATAAT
6835 AATAA
1 AATAA
6840 AGATAGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 19 0.68
15 9 0.32
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (14 bp):
AATAACAAAATAAT
Found at i:6820 original size:17 final size:17
Alignment explanation
Indices: 6792--6839 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
6782 GCTAAAAAAA
*
6792 AATAACAAAAATAATAAT
1 AATAA-AAAAATAATAAC
6810 AATAAAAAAATAATAAC
1 AATAAAAAAATAATAAC
* *
6827 AACAATAAAATAA
1 AATAAAAAAATAA
6840 AGATAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (17 bp):
AATAAAAAAATAATAAC
Found at i:6822 original size:26 final size:25
Alignment explanation
Indices: 6787--6840 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
6777 CCCTTGCTAA
*
6787 AAAAAAATAACAAAAATAATAATAAT
1 AAAAAAATAACAAAAACAATAA-AAT
* *
6813 AAAAAAATAATAACAACAATAAAAT
1 AAAAAAATAACAAAAACAATAAAAT
6838 AAA
1 AAA
6841 GATAGAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (25 bp):
AAAAAAATAACAAAAACAATAAAAT
Found at i:6825 original size:29 final size:27
Alignment explanation
Indices: 6784--6839 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
6774 AACCCCTTGC
6784 TAAAAAAAAATAACAAAAATAATAATAA
1 TAAAAAAAAATAACAAAAATAA-AATAA
*
6812 TAAAAAAATAATAACAACAATAAAATAA
1 TAAAAAAA-AATAACAAAAATAAAATAA
6840 AGATAGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (27 bp):
TAAAAAAAAATAACAAAAATAAAATAA
Found at i:7581 original size:24 final size:23
Alignment explanation
Indices: 7524--7581 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 23
7514 AATTATTATA
*
7524 TTATATATTA--TAATTGAACTT
1 TTATATATTATTTAATTGAACAT
* * *
7545 TTTTAGATCATTTCAATTGAACAT
1 TTATATATTATTT-AATTGAACAT
7569 TTATATATTATTT
1 TTATATATTATTT
7582 TGAGACTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
21 7 0.26
23 1 0.04
24 19 0.70
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.53
Consensus pattern (23 bp):
TTATATATTATTTAATTGAACAT
Found at i:9092 original size:22 final size:23
Alignment explanation
Indices: 9051--9093 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9041 AAAATAATTA
* *
9051 AAAATTAAAAAAATCAGAAAAAC
1 AAAATAAAAAAAAACAGAAAAAC
9074 AAAATAAAAAAAAAC-GAAAA
1 AAAATAAAAAAAAACAGAAAA
9094 TCAGATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.79, C:0.07, G:0.05, T:0.09
Consensus pattern (23 bp):
AAAATAAAAAAAAACAGAAAAAC
Found at i:9220 original size:19 final size:19
Alignment explanation
Indices: 9176--9220 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
9166 CTTTTCTTCT
*
9176 TCTTCTCGAGCTTCTCCCT
1 TCTTCTCGAGCTTCTCCCA
* * *
9195 TCATCTCGAGGTTCTTCCA
1 TCTTCTCGAGCTTCTCCCA
9214 TCTTCTC
1 TCTTCTC
9221 ATTATGCCAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.09, C:0.38, G:0.11, T:0.42
Consensus pattern (19 bp):
TCTTCTCGAGCTTCTCCCA
Done.