Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022220.1 Corchorus olitorius cultivar O-4 contig22253, 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: 26732
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Found at i:7204 original size:11 final size:11
Alignment explanation
Indices: 7188--7213 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7178 GTTGTAGATC
7188 TTTTCTTCTAG
1 TTTTCTTCTAG
7199 TTTTCTTCTAG
1 TTTTCTTCTAG
7210 TTTT
1 TTTT
7214 TTAGGCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:11276 original size:138 final size:138
Alignment explanation
Indices: 11028--11303 Score: 480
Period size: 138 Copynumber: 2.0 Consensus size: 138
11018 CGCCGAGACA
* * *
11028 CATGCTCGGCCACAACTCGGCCACCTAAGCCATCTGCCTGGCCACACCCGGACTCGTCCGCGCAC
1 CATGCCCGGCCACAACTCGGCCACCCAAGCCATCTGCCTGGCCACACCCAGACTCGTCCGCGCAC
*
11093 CAAGCCCGGCCATCCGCGCCGCCTGCCCGGTTGAAACTGCCTTCCTCCGCGCCATCCGAGCCTCA
66 CAAGCCCGGCCATCCACGCCGCCTGCCCGGTTGAAACTGCCTTCCTCCGCGCCATCCGAGCCTCA
11158 TGCCCGGC
131 TGCCCGGC
*
11166 CATGCCCGGCCACAACTCGGCCACCCGAGCCATCTGCCTGGCCACACCCAGACTCGTCCGCGCAC
1 CATGCCCGGCCACAACTCGGCCACCCAAGCCATCTGCCTGGCCACACCCAGACTCGTCCGCGCAC
* * *
11231 CAAGCCCGTCCATCCACGCCGCCTGCCCGGTTGAAACTGCCTTCCTCCGCGCCATTCGCGCCTCA
66 CAAGCCCGGCCATCCACGCCGCCTGCCCGGTTGAAACTGCCTTCCTCCGCGCCATCCGAGCCTCA
11296 TGCCCGGC
131 TGCCCGGC
11304 TAGGACAAGA
Statistics
Matches: 130, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 130 1.00
ACGTcount: A:0.15, C:0.48, G:0.22, T:0.14
Consensus pattern (138 bp):
CATGCCCGGCCACAACTCGGCCACCCAAGCCATCTGCCTGGCCACACCCAGACTCGTCCGCGCAC
CAAGCCCGGCCATCCACGCCGCCTGCCCGGTTGAAACTGCCTTCCTCCGCGCCATCCGAGCCTCA
TGCCCGGC
Found at i:11502 original size:21 final size:21
Alignment explanation
Indices: 11461--11506 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
11451 CTCATTCACT
**
11461 GTGCCACCACCGGTTAAGCCC
1 GTGCCACCACCGGCCAAGCCC
*
11482 GTGCCACCACCGGCCATGCCC
1 GTGCCACCACCGGCCAAGCCC
11503 GTGC
1 GTGC
11507 AATCACCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.46, G:0.26, T:0.13
Consensus pattern (21 bp):
GTGCCACCACCGGCCAAGCCC
Found at i:19219 original size:30 final size:30
Alignment explanation
Indices: 19151--19221 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
19141 TATATATATA
*
19151 TGAAAAAAAAAATTACTCTGGTAATATTGG
1 TGAAAAAAAAAATTACTCTGGTAATATTAG
**
19181 TGCCAAAAAAAATTACTCTGGTAATATTAAG
1 TGAAAAAAAAAATTACTCTGGTAATATT-AG
19212 -GAAAAAAAAA
1 TGAAAAAAAAA
19222 CCTTGAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (30 bp):
TGAAAAAAAAAATTACTCTGGTAATATTAG
Found at i:19782 original size:20 final size:20
Alignment explanation
Indices: 19744--19782 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19734 CAACTCGAGA
*
19744 AAAATTCGAGTTCGACTCGG
1 AAAATTCGAGTCCGACTCGG
19764 AAAATTCGAG-CCGAGCTCG
1 AAAATTCGAGTCCGA-CTCG
19783 AGCTCGAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.21
Consensus pattern (20 bp):
AAAATTCGAGTCCGACTCGG
Found at i:20868 original size:96 final size:98
Alignment explanation
Indices: 20695--20876 Score: 280
Period size: 98 Copynumber: 1.9 Consensus size: 98
20685 TTTTGAGGTA
* * * * *
20695 GAGGCAGAGGCAGAGATGAGAGAAAAAAAAAAAAAGAAAGGCAGAGGTAGAGTTCGCAGCGCTGA
1 GAGGCAGAGGCAGAGATGAGAGAAAAAAAAAAAAAGAAAGGCAAAGGCAGAGTGCACAGCGCAGA
20760 GAGGAAAGAAGAAAAAGAAATCGAAAGGGTTTT
66 GAGGAAAGAAGAAAAAGAAATCGAAAGGGTTTT
*
20793 GAGGCAGAGGCAGAGATGAGAGAAAAAAAAAAAGGAGAAA-G-AAAGGCAGAG-GCACAGCGCAG
1 GAGGCAGAGGCAGAGATGAGAGAAAAAAAAAAA-AAGAAAGGCAAAGGCAGAGTGCACAGCGCAG
20855 AGAGGAAAGAAGAAAAAGAAAT
65 AGAGGAAAGAAGAAAAAGAAAT
20877 TATTTAGGGA
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
96 30 0.39
97 8 0.10
98 34 0.44
99 5 0.06
ACGTcount: A:0.51, C:0.08, G:0.34, T:0.07
Consensus pattern (98 bp):
GAGGCAGAGGCAGAGATGAGAGAAAAAAAAAAAAAGAAAGGCAAAGGCAGAGTGCACAGCGCAGA
GAGGAAAGAAGAAAAAGAAATCGAAAGGGTTTT
Found at i:20944 original size:20 final size:20
Alignment explanation
Indices: 20912--20957 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
20902 TTTATATTTT
20912 TATAAATACTAAACA-TAATA
1 TATAAATACTAAACACTAA-A
*
20932 TATAAATTA-TAAATACTAAA
1 TATAAA-TACTAAACACTAAA
20952 TATAAA
1 TATAAA
20958 AAATATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAATACTAAACACTAAA
Found at i:22364 original size:134 final size:133
Alignment explanation
Indices: 22110--22350 Score: 353
Period size: 134 Copynumber: 1.8 Consensus size: 133
22100 TTGTTTAAAG
*
22110 TTTTATAATTTTATTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
* * *
22175 ATTTTATTTTTACCAGTTTATTATTTTATTTTAATTTAAAAACTTAAATATTAAAATTTTTTAAA
66 ATTTTATTTTTACCAGTTTACTAATTTATATTAA--TAAAAACTTAAATATTAAAATTTTTTAAA
22240 TATAT
129 TATAT
* * * **
22245 TTTTATAGTTTTACTCAATTAAAAACTCTA-TTTTTATTTTATTAAATCTAATATTTTTATAACT
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
*
22309 ATTTTATTTTTACCATTTTACTAATTTA-ATTAA-AAAAACTTA
66 ATTTTATTTTTACCAGTTTACTAATTTATATTAATAAAAACTTA
22351 TAAAGTTTTT
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
130 9 0.09
133 4 0.04
134 56 0.58
135 27 0.28
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (133 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
ATTTTATTTTTACCAGTTTACTAATTTATATTAATAAAAACTTAAATATTAAAATTTTTTAAATA
TAT
Found at i:22627 original size:16 final size:16
Alignment explanation
Indices: 22584--22618 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
22574 TTTGGCCTCA
*
22584 GGTCACTCGGGTTTTG
1 GGTCATTCGGGTTTTG
22600 GGTCATTCGGGTTTTG
1 GGTCATTCGGGTTTTG
22616 GGT
1 GGT
22619 TTTTCGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.14, G:0.40, T:0.40
Consensus pattern (16 bp):
GGTCATTCGGGTTTTG
Found at i:24741 original size:13 final size:13
Alignment explanation
Indices: 24699--24742 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
24689 AATTTTTTTT
24699 AAAAAGAAAACAGA
1 AAAAAGAAAA-AGA
24713 AAAAAGAAAAAGGA
1 AAAAAGAAAAA-GA
**
24727 AAAAATTAAAAGA
1 AAAAAGAAAAAGA
24740 AAA
1 AAA
24743 TAATAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Done.