Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019300.1 Corchorus olitorius cultivar O-4 contig19333, 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: 12733
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:2151 original size:41 final size:40
Alignment explanation
Indices: 2059--2155 Score: 99
Period size: 41 Copynumber: 2.4 Consensus size: 40
2049 AGTAAAATCT
* * *
2059 TAAATCATGGG-CAAAATTTAATCAATTAACAAATAAACAT
1 TAAATCA-GGGACTAAATTGAATCAATTAACAAATAAACAC
* *
2099 TCCAATTAGGGACTAAATTGAATCAATTAACGAACATAAAC-C
1 T-AAATCAGGGACTAAATTGAATCAATTAAC-AA-ATAAACAC
2141 TAAATCAGGGACTAA
1 TAAATCAGGGACTAA
2156 GGTGAAAACG
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
40 4 0.09
41 33 0.72
42 3 0.07
43 6 0.13
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.25
Consensus pattern (40 bp):
TAAATCAGGGACTAAATTGAATCAATTAACAAATAAACAC
Found at i:4499 original size:19 final size:19
Alignment explanation
Indices: 4475--4525 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
4465 CTAAAGTTAA
4475 AATGCCTAAATGCAAGCCC
1 AATGCCTAAATGCAAGCCC
* *
4494 AATGCCCAAGTGCAAGCCC
1 AATGCCTAAATGCAAGCCC
*
4513 AAAG-CTAAATGCA
1 AATGCCTAAATGCA
4526 TCTAATATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (19 bp):
AATGCCTAAATGCAAGCCC
Found at i:4891 original size:26 final size:26
Alignment explanation
Indices: 4840--4935 Score: 138
Period size: 26 Copynumber: 3.6 Consensus size: 26
4830 AATGAAAAAA
4840 AAATGACCAAAATGCCCCCTGAAGTAC
1 AAATGACCAAAATG-CCCCTGAAGTAC
*
4867 AAATGACCAAAATGCCCCTGAAGTAA
1 AAATGACCAAAATGCCCCTGAAGTAC
**
4893 AAATGACCAAAATGCCCCTGAATGCGC
1 AAATGACCAAAATGCCCCTGAA-GTAC
4920 AAAATGACCAAAATGC
1 -AAATGACCAAAATGC
4936 TCCTAGATGA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
26 33 0.52
27 15 0.24
28 15 0.24
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.15
Consensus pattern (26 bp):
AAATGACCAAAATGCCCCTGAAGTAC
Found at i:8062 original size:33 final size:33
Alignment explanation
Indices: 8025--8089 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
8015 TATTGATTAT
8025 ACTAAACCTAATTTAAGTGTTGTTTGTGATGAC
1 ACTAAACCTAATTTAAGTGTTGTTTGTGATGAC
* ** *
8058 ACTAAATCTGTTTTAGGTGTTGTTTGTGATGA
1 ACTAAACCTAATTTAAGTGTTGTTTGTGATGA
8090 AACAAATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (33 bp):
ACTAAACCTAATTTAAGTGTTGTTTGTGATGAC
Found at i:8101 original size:33 final size:32
Alignment explanation
Indices: 8036--8135 Score: 112
Period size: 33 Copynumber: 3.0 Consensus size: 32
8026 CTAAACCTAA
* *
8036 TTTAAGTGTTGTTTGTGATGACACTAAATCTGT
1 TTTAGGTGTTGTTTGTGATGAAAC-AAATCTGT
8069 TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
1 TTTAGGTGTTGTTTGTGATGAAACAAA-TCTGT
* * *
8102 TTT-GGATGCTATTCGTGATGAAAACAAATCTGT
1 TTTAGG-TGTTGTTTGTGATG-AAACAAATCTGT
8135 T
1 T
8136 ATGGTTGATC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
32 5 0.08
33 47 0.80
34 7 0.12
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (32 bp):
TTTAGGTGTTGTTTGTGATGAAACAAATCTGT
Found at i:9973 original size:21 final size:20
Alignment explanation
Indices: 9944--9986 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
9934 ATACTCACAA
*
9944 AGAAGTTTCAAGCTCATTGG
1 AGAAGTTTCAAACTCATTGG
9964 AGAAGGTTTCAAACTCATTGG
1 AGAA-GTTTCAAACTCATTGG
9985 AG
1 AG
9987 TTGCCTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (20 bp):
AGAAGTTTCAAACTCATTGG
Done.