Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012410.1 Corchorus olitorius cultivar O-4 contig12443, 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: 25710
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1159 original size:177 final size:178
Alignment explanation
Indices: 849--1188 Score: 479
Period size: 177 Copynumber: 1.9 Consensus size: 178
839 TTCCACCAAA
* * * *
849 AGCACAAATTATGTAATATTAAGTAGACCGTCTATTTACGTTAACCGAAACAATTAATTCCTTAG
1 AGCACAAATTATATAATATTAAGTAGACCGTCTATTCACGTTAACCAAAACAATCAATTCCTTAG
* * *
914 AAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTGCATGAAAGTTGTAGATCAT
66 AAGCATTTTTGATACATTGAACATTAAATTTAGCTTTCGAGTCCTGCATGAAAGTTGTAGATCAT
* *
979 GGAATAACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATATGG
131 GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATCAGACATATGG
* ** *
1027 AGCA-AAAGTTATATAATATTAAGTGGACCGTCTATTCACGTTAACCAAAACAA-CAATTTTTTG
1 AGCACAAA-TTATATAATATTAAGTAGACCGTCTATTCACGTTAACCAAAACAATCAATTCCTTA
* *
1090 GAAGCATTTTTGATA-ATTGAAACATTAAATTTAGCTTTCGAGTCCTTCGTGAAAGTTGTAGATC
65 GAAGCATTTTTGATACATTG-AACATTAAATTTAGCTTTCGAGTCCTGCATGAAAGTTGTAGATC
* * *
1154 ATGGAACAATCTTTTAATAGACACTTAAATCATCT
129 ATGGAACAACCTTTCAAGAGACACTTAAATCATCT
1189 GAATTGAATA
Statistics
Matches: 142, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
176 3 0.02
177 94 0.66
178 45 0.32
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (178 bp):
AGCACAAATTATATAATATTAAGTAGACCGTCTATTCACGTTAACCAAAACAATCAATTCCTTAG
AAGCATTTTTGATACATTGAACATTAAATTTAGCTTTCGAGTCCTGCATGAAAGTTGTAGATCAT
GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATCAGACATATGG
Found at i:2431 original size:23 final size:24
Alignment explanation
Indices: 2386--2434 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
2376 AACTATAGCA
2386 AATAATAAAGAAAACAATAATAAG
1 AATAATAAAGAAAACAATAATAAG
2410 AATAATAAAGAAAA-AATAATAAG
1 AATAATAAAGAAAACAATAATAAG
2433 AA
1 AA
2435 AGCATATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (24 bp):
AATAATAAAGAAAACAATAATAAG
Found at i:3127 original size:11 final size:11
Alignment explanation
Indices: 3111--3135 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3101 CCCTCTTTTT
3111 AAACTAGAGAA
1 AAACTAGAGAA
3122 AAACTAGAGAA
1 AAACTAGAGAA
3133 AAA
1 AAA
3136 TAAAAGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAACTAGAGAA
Found at i:6197 original size:2 final size:2
Alignment explanation
Indices: 6190--6218 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6180 GCTAAAATTA
6190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6219 AAAGTCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6369 original size:127 final size:129
Alignment explanation
Indices: 6195--6451 Score: 437
Period size: 128 Copynumber: 2.0 Consensus size: 129
6185 AATTAATATA
* *
6195 TATATATATATATATATATATATAAAAGTCTAAACTTCAAAAACCTTGATCTGAAATATCTAAAA
1 TATATATATATATATATATATATAAAACTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAA
* *
6260 TA-TCCTTTTAATATTAAACATGAGTTTTAAGCTTTAGTGGTTAATATGTAATTTAAATTACAC
66 TACCCCTTTTAATATTAAACATGAGTTTTAACCTTTAGTGGTTAATATGTAATTTAAATTACAC
* *
6323 TATATATATATATATA-ATATATATAACTCTATACTTCAAAAACCTTGACCTGAAATATCTAAAA
1 TATATATATATATATATATATATAAAACTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAA
*
6387 TACCCCTTTTAATATTAAACATGAGTTTTAACCTTTAGTGGTTAATATGTAATTTAAATTGCAC
66 TACCCCTTTTAATATTAAACATGAGTTTTAACCTTTAGTGGTTAATATGTAATTTAAATTACAC
6451 T
1 T
6452 CCAATAAAAT
Statistics
Matches: 121, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
127 46 0.38
128 75 0.62
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (129 bp):
TATATATATATATATATATATATAAAACTCTAAACTTCAAAAACCTTGACCTGAAATATCTAAAA
TACCCCTTTTAATATTAAACATGAGTTTTAACCTTTAGTGGTTAATATGTAATTTAAATTACAC
Found at i:6475 original size:2 final size:2
Alignment explanation
Indices: 6464--6498 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6454 AATAAAATCT
6464 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6499 CTACATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17693 original size:33 final size:33
Alignment explanation
Indices: 17651--17717 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
17641 TACAAGGTTG
* *
17651 ATGTCTATAGGTATTTCTTCTTTCTATTTTCTA
1 ATGTCTATAGGAAATTCTTCTTTCTATTTTCTA
17684 ATGTCTATAGGAAATTCTTCTTTCTATTTTCTA
1 ATGTCTATAGGAAATTCTTCTTTCTATTTTCTA
17717 A
1 A
17718 AATCAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.15, G:0.09, T:0.54
Consensus pattern (33 bp):
ATGTCTATAGGAAATTCTTCTTTCTATTTTCTA
Found at i:20537 original size:16 final size:16
Alignment explanation
Indices: 20512--20564 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
20502 TACCCTTATC
20512 TTTTTATTTTTCGTTA
1 TTTTTATTTTTCGTTA
* *
20528 TTTTTCTTTTTC-TTT
1 TTTTTATTTTTCGTTA
20543 TATTTTATTTTT-GTTTA
1 T-TTTTATTTTTCG-TTA
20560 TTTTT
1 TTTTT
20565 CTTAGTTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (16 bp):
TTTTTATTTTTCGTTA
Found at i:21733 original size:21 final size:20
Alignment explanation
Indices: 21694--21742 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
21684 TCAATGCTTT
**
21694 AAGAATGCAAGAGGGATTTCA
1 AAGAA-GCAAGAGCCATTTCA
*
21715 AAGGAAGCAAGAGCCATTTCC
1 AA-GAAGCAAGAGCCATTTCA
21736 AAGAAGC
1 AAGAAGC
21743 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 16 0.67
22 3 0.12
ACGTcount: A:0.43, C:0.16, G:0.27, T:0.14
Consensus pattern (20 bp):
AAGAAGCAAGAGCCATTTCA
Done.