Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010771.1 Corchorus capsularis cultivar CVL-1 contig10792, 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: 27708
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:984 original size:22 final size:22
Alignment explanation
Indices: 956--999 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
946 TTATTTAAAG
956 GCATGCCCCATTTTTGCAACCT
1 GCATGCCCCATTTTTGCAACCT
978 GCATGCCCCATTTTTGCAACCT
1 GCATGCCCCATTTTTGCAACCT
1000 ATCTTTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.14, T:0.32
Consensus pattern (22 bp):
GCATGCCCCATTTTTGCAACCT
Found at i:11739 original size:17 final size:18
Alignment explanation
Indices: 11714--11748 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
11704 GGGATTATTA
11714 TTATCATTTA-ATTTTAT
1 TTATCATTTATATTTTAT
*
11731 TTATTATTTATATTTTAT
1 TTATCATTTATATTTTAT
11749 AGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATCATTTATATTTTAT
Found at i:15171 original size:28 final size:25
Alignment explanation
Indices: 15115--15163 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
15105 TTATTTATTT
15115 TAAAAAAAATAATAACATATATAAA
1 TAAAAAAAATAATAACATATATAAA
15140 TAAAAAAAATACAATAA-ATATATA
1 TAAAAAAAAT--AATAACATATATA
15164 TGCATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (25 bp):
TAAAAAAAATAATAACATATATAAA
Found at i:15322 original size:62 final size:63
Alignment explanation
Indices: 15252--15383 Score: 160
Period size: 62 Copynumber: 2.1 Consensus size: 63
15242 GGTTGGCTAT
* * *
15252 TATGATCATGCAAGAGCATCGTTTAAGCATACTTACAT-GTTTATCA-TTTTTCAATGGTAGTA
1 TATGATCATGCAAGAGAATCATTTAAGCATACCTACATCGTTTATCACTTTTT-AATGGTAGTA
* * * *
15314 TATGATCATGCAAGAGAATTATTTAAGCATGCCTACATACCTTTTATCACTTTTTAGTGGTAGTA
1 TATGATCATGCAAGAGAATCATTTAAGCATACCTACAT--CGTTTATCACTTTTTAATGGTAGTA
15379 TATGA
1 TATGA
15384 CTAGCACTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
62 33 0.56
65 21 0.36
66 5 0.08
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (63 bp):
TATGATCATGCAAGAGAATCATTTAAGCATACCTACATCGTTTATCACTTTTTAATGGTAGTA
Found at i:16333 original size:29 final size:29
Alignment explanation
Indices: 16299--16398 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
16289 CCTCATGACG
*
16299 GGCCGTAAGACCGACGAGCATTCATTGTC
1 GGCCGTAAGACCGAAGAGCATTCATTGTC
* * ** *
16328 GGCCGTAAGACCTCATGA-CGGTCA-TGAC
1 GGCCGTAAGACC-GAAGAGCATTCATTGTC
* *
16356 GGCTCGTAAGACCGAAGAGCATTTATTCTC
1 GGC-CGTAAGACCGAAGAGCATTCATTGTC
*
16386 GACCGTAAGACCG
1 GGCCGTAAGACCG
16399 CATGACGTGT
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
28 9 0.17
29 38 0.70
30 7 0.13
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.20
Consensus pattern (29 bp):
GGCCGTAAGACCGAAGAGCATTCATTGTC
Found at i:16364 original size:58 final size:58
Alignment explanation
Indices: 16291--16405 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
16281 CAGTAAGACC
* * * *
16291 TCATGACGGGCCGTAAGACCGACGAGCATTCATTGTCGGCCGTAAGACCTCATGACGG
1 TCATGACGGGCCGTAAGACCGAAGAGCATTCATTCTCGACCGTAAGACCGCATGACGG
*
16349 TCATGAC-GGCTCGTAAGACCGAAGAGCATTTATTCTCGACCGTAAGACCGCATGACG
1 TCATGACGGGC-CGTAAGACCGAAGAGCATTCATTCTCGACCGTAAGACCGCATGACG
16406 TGTTGTAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 3 0.06
58 48 0.94
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.20
Consensus pattern (58 bp):
TCATGACGGGCCGTAAGACCGAAGAGCATTCATTCTCGACCGTAAGACCGCATGACGG
Found at i:16515 original size:50 final size:51
Alignment explanation
Indices: 16388--16627 Score: 227
Period size: 50 Copynumber: 4.8 Consensus size: 51
16378 TTATTCTCGA
* * * * *
16388 CCGTAAGACCGCATGACGTGTTGTAAGACCAACGAGTATCT-ACCGATCGA
1 CCGTAAGACCCCATGACGGGTCGTAAGACCGACGAGTATCTAACCGATCGG
* * * *
16438 CCGTAAAACCCCATAACGGGCCATAAGACCGACGAGTATCT-ACCGATCGG
1 CCGTAAGACCCCATGACGGGTCGTAAGACCGACGAGTATCTAACCGATCGG
* * * * * *
16488 TCGTAAGACCCCATGATGGGTCGTAAGACCGATGGGCAT-TAATCGATCGG
1 CCGTAAGACCCCATGACGGGTCGTAAGACCGACGAGTATCTAACCGATCGG
* * * * *
16538 CGGTAAGACCCCATGACGAGTCGTAAGACCGACGAGCAT-TGACCGACCGG
1 CCGTAAGACCCCATGACGGGTCGTAAGACCGACGAGTATCTAACCGATCGG
* * * * *
16588 CCATAAGACCCCATGATGGGCCGTAAGACCAACAAGTATC
1 CCGTAAGACCCCATGACGGGTCGTAAGACCGACGAGTATC
16628 ATCAACAACG
Statistics
Matches: 152, Mismatches: 36, Indels: 3
0.80 0.19 0.02
Matches are distributed among these distances:
49 1 0.01
50 151 0.99
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (51 bp):
CCGTAAGACCCCATGACGGGTCGTAAGACCGACGAGTATCTAACCGATCGG
Found at i:16535 original size:100 final size:100
Alignment explanation
Indices: 16431--16617 Score: 250
Period size: 100 Copynumber: 1.9 Consensus size: 100
16421 GAGTATCTAC
* * * * *
16431 CGATCGACCGTAAAACCCCATAACGGGCCATAAGACCGACGAGTATCT-ACCGATCGGTCGTAAG
1 CGATCGACCGTAAAACCCCATAACGAGCCATAAGACCGACGAGCAT-TGACCGACCGGCCATAAG
*
16495 ACCCCATGATGGGTCGTAAGACCGATGGGCATTAAT
65 ACCCCATGATGGGCCGTAAGACCGATGGGCATTAAT
* * * * * *
16531 CGATCGGCGGTAAGACCCCATGACGAGTCGTAAGACCGACGAGCATTGACCGACCGGCCATAAGA
1 CGATCGACCGTAAAACCCCATAACGAGCCATAAGACCGACGAGCATTGACCGACCGGCCATAAGA
16596 CCCCATGATGGGCCGTAAGACC
66 CCCCATGATGGGCCGTAAGACC
16618 AACAAGTATC
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 1 0.01
100 73 0.99
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (100 bp):
CGATCGACCGTAAAACCCCATAACGAGCCATAAGACCGACGAGCATTGACCGACCGGCCATAAGA
CCCCATGATGGGCCGTAAGACCGATGGGCATTAAT
Found at i:16938 original size:116 final size:115
Alignment explanation
Indices: 16727--17137 Score: 491
Period size: 116 Copynumber: 3.5 Consensus size: 115
16717 CAACGAATAA
* ** * *
16727 CCCTCTTAAGGGT-CTGATGATACCGATTGGTAGGCGGTGGAGGGCCGACCTCGACCAAGCACGA
1 CCCTCTTAAGGGTCCAG-TGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTCGACCAAGCACG-
* * * *
16791 TCCCGGCTGGTTGGCGGTGGAGAGTCTACCTTGACCAAGCACGGATGAAGAG
64 TCCCGGCTGGTAGGCGGTGAAGAGCCCACCTTGACCAAGCACGGATGAAGAG
* ** * *
16843 CCCTCTTAAGGGTCCATTGATACCGGCTGGCAGGCAATGGAGAACCGACCTTGACCAAGCACAGT
1 CCCTCTTAAGGGTCCAGTGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTCGACCAAGCAC-GT
* * ** * *
16908 CCCGGCTGGCAGGCGGTGAAGAGCCGACCTTGATTAAGCACGAATGGAGAG
65 CCCGGCTGGTAGGCGGTGAAGAGCCCACCTTGACCAAGCACGGATGAAGAG
* * *
16959 CCTTCTTAAGGGTCCAGTGATACCAGCTGGCAGGCGGTGGAGAGCCGACCTCAACCAAGCACGGT
1 CCCTCTTAAGGGTCCAGTGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTCGACCAAGCAC-GT
* * * * *
17024 CCCGACTAGTAGGCAGTGTAGAGCCCACCTTGACCAAGAACGGATGAAGAG
65 CCCGGCTGGTAGGCGGTGAAGAGCCCACCTTGACCAAGCACGGATGAAGAG
* ** *
17075 CCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGGTGACCTTGACCAAGCACG
1 CCCTCTTAAGGGTCCAGTGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTCGACCAAGCACG
17138 AATGATGAAC
Statistics
Matches: 247, Mismatches: 46, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
115 1 0.00
116 244 0.99
117 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.17
Consensus pattern (115 bp):
CCCTCTTAAGGGTCCAGTGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTCGACCAAGCACGTC
CCGGCTGGTAGGCGGTGAAGAGCCCACCTTGACCAAGCACGGATGAAGAG
Found at i:17130 original size:72 final size:72
Alignment explanation
Indices: 17050--17205 Score: 177
Period size: 72 Copynumber: 2.2 Consensus size: 72
17040 TGTAGAGCCC
* * * * *
17050 ACCTTGACCAAGAACGGATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGG
1 ACCTTGACCAAGAACGAATGAAGAACCCTCTTAAGGGTCCAGAGAGACCGGCTGGCAGGCGATGA
17115 AGAGGTG
66 AGAGGTG
* * * * ** *
17122 ACCTTGACCAAGCACGAATGATGAACCCTCTTCAGGTTTTAGTGAGACCGGCTGGCAGGCGATGA
1 ACCTTGACCAAGAACGAATGAAGAACCCTCTTAAGGGTCCAGAGAGACCGGCTGGCAGGCGATGA
*
17187 AGAGTTG
66 AGAGGTG
* *
17194 ATCTTAACCAAG
1 ACCTTGACCAAG
17206 CACGTCACCG
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (72 bp):
ACCTTGACCAAGAACGAATGAAGAACCCTCTTAAGGGTCCAGAGAGACCGGCTGGCAGGCGATGA
AGAGGTG
Found at i:21828 original size:3 final size:3
Alignment explanation
Indices: 21820--21846 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21810 GAATTAGTCG
21820 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
21847 CTCTCTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:26653 original size:10 final size:10
Alignment explanation
Indices: 26638--26676 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
26628 CTCTTTCTTA
26638 TTGTTATAGG
1 TTGTTATAGG
*
26648 TTGTTATTATG
1 TTGTTA-TAGG
26659 TTGTTATAGG
1 TTGTTATAGG
*
26669 TTCTTATA
1 TTGTTATA
26677 TTTTGAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.56
Consensus pattern (10 bp):
TTGTTATAGG
Done.