Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005962.1 Corchorus capsularis cultivar CVL-1 contig05980, 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: 19109
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Found at i:3983 original size:27 final size:28
Alignment explanation
Indices: 3921--3975 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
3911 TGAATTAGTA
*
3921 AAATGACCAAAATACCCCCTAGATGCAC
1 AAATGACCAAAATAACCCCTAGATGCAC
*
3949 AAATGACCAAAA-AACCCCTGGATGCAC
1 AAATGACCAAAATAACCCCTAGATGCAC
3976 CGATGACCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.44, C:0.31, G:0.13, T:0.13
Consensus pattern (28 bp):
AAATGACCAAAATAACCCCTAGATGCAC
Found at i:7615 original size:31 final size:30
Alignment explanation
Indices: 7575--7653 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 30
7565 ATTTTTAGCC
*
7575 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
1 ACCAATTTGAG-CTAAACCTTTCAAAACTTG
7606 -CTCAATTTGAGCATAAACCTTTCAAAACTTG
1 AC-CAATTTGAGC-TAAACCTTTCAAAACTTG
7637 ACCAATTTGAGCCTAAA
1 ACCAATTTGAG-CTAAA
7654 AATAGGTGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
30 2 0.05
31 39 0.91
32 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (30 bp):
ACCAATTTGAGCTAAACCTTTCAAAACTTG
Found at i:15417 original size:6 final size:6
Alignment explanation
Indices: 15399--15441 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
15389 GTTCAAGTGC
* * *
15399 TTGGAG TTAGAG TTGGAG TTGGAG TTGGAG TGGGAG TGGGAG T
1 TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG T
15442 GGGGAGTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.19, C:0.00, G:0.51, T:0.30
Consensus pattern (6 bp):
TTGGAG
Found at i:17319 original size:36 final size:36
Alignment explanation
Indices: 17274--17445 Score: 204
Period size: 36 Copynumber: 4.7 Consensus size: 36
17264 GCAGTCAAAG
*
17274 GAACTTAATTCAGGGAAATTAAGTAAAAGTAGTTAA
1 GAACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAA
* *
17310 GAACTTAATTCAGGGAAATTAGGTAAAAACAGTTAAA
1 GAACTTAATTCAGGGAAATTAAGTAAAAGCAGTT-AA
*
17347 GTACTTAATTCA-GGATAATTAAGTAAAAGCAGTT-A
1 GAACTTAATTCAGGGA-AATTAAGTAAAAGCAGTTAA
* * *
17382 GAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAA
1 G-A-ACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAA
* **
17420 GGACTTAATTCAGGGTGATTAAGTAA
1 GAACTTAATTCAGGGAAATTAAGTAA
17446 GAAAAGCACA
Statistics
Matches: 118, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
35 2 0.02
36 57 0.48
37 55 0.47
38 4 0.03
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (36 bp):
GAACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAA
Found at i:17367 original size:37 final size:35
Alignment explanation
Indices: 17252--17433 Score: 186
Period size: 37 Copynumber: 4.9 Consensus size: 35
17242 CATCGTATGC
* *
17252 ATTAAGTAAAGTGCAGTCAAAGGAACTTAATTCAGGGAA
1 ATTAAGTAAA-AGCAGTTAAA-G-ACTTAATTCA-GGAA
*
17291 ATTAAGTAAAAGTAGTT-AAGAACTTAATTCAGGGAA
1 ATTAAGTAAAAGCAGTTAAAG-ACTTAATTCA-GGAA
* *
17327 ATTAGGTAAAAACAGTTAAAGTACTTAATTCAGGATA
1 ATTAAGTAAAAGCAGTTAAAG-ACTTAATTCAGGA-A
*
17364 ATTAAGTAAAAGCAGTTAGAAGACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTTA-AAGACTTAATTCA-GGAA
* * *
17401 ATTAAGTAAAATCAGTCAAGGACTTAATTCAGG
1 ATTAAGTAAAAGCAGTTAAAGACTTAATTCAGG
17434 GTGATTAAGT
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
35 2 0.02
36 46 0.37
37 59 0.47
38 9 0.07
39 10 0.08
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.27
Consensus pattern (35 bp):
ATTAAGTAAAAGCAGTTAAAGACTTAATTCAGGAA
Found at i:17426 original size:73 final size:72
Alignment explanation
Indices: 17252--17445 Score: 230
Period size: 73 Copynumber: 2.6 Consensus size: 72
17242 CATCGTATGC
* *
17252 ATTAAGTAAAGTGCAGTCAAAGGAACTTAATTCAGGGA-AATTAAGTAAAAGTAGTTAAGAACTT
1 ATTAAGTAAAAT-CAGTC-AAGG-ACTTAATTCA-GGATAATTAAGTAAAAGCAGTTAAGAACTT
17316 AATTCAGGGAA
62 AATTCAGGGAA
* * * *
17327 ATTAGGTAAAAACAGTTAAAGTACTTAATTCAGGATAATTAAGTAAAAGCAGTT-AGAAGACTTA
1 ATTAAGTAAAATCAG-TCAAGGACTTAATTCAGGATAATTAAGTAAAAGCAGTTAAG-A-ACTTA
*
17391 ATTCAGGGTA
63 ATTCAGGGAA
* *
17401 ATTAAGTAAAATCAGTCAAGGACTTAATTCAGGGTGATTAAGTAA
1 ATTAAGTAAAATCAGTCAAGGACTTAATTCAGGATAATTAAGTAA
17446 GAAAAGCACA
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
72 5 0.05
73 54 0.53
74 33 0.32
75 10 0.10
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.27
Consensus pattern (72 bp):
ATTAAGTAAAATCAGTCAAGGACTTAATTCAGGATAATTAAGTAAAAGCAGTTAAGAACTTAATT
CAGGGAA
Found at i:17506 original size:41 final size:41
Alignment explanation
Indices: 17444--17546 Score: 188
Period size: 41 Copynumber: 2.5 Consensus size: 41
17434 GTGATTAAGT
* *
17444 AAGAAAAGCACAGACTTAATTTCAAGGAACGAAATTAGGTA
1 AAGACAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
17485 AAGACAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
1 AAGACAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
17526 AAGACAAGCACAGACTTAATT
1 AAGACAAGCACAGACTTAATT
17547 CAGGGTAATT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (41 bp):
AAGACAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
Found at i:17756 original size:37 final size:37
Alignment explanation
Indices: 17643--17938 Score: 309
Period size: 37 Copynumber: 8.4 Consensus size: 37
17633 AGAACAGACA
* **
17643 AAGGACTTAATTCCAAGGAAAGGGAATTAAGTAGAGCA
1 AAGGACTTAATTCCAAGG-AAGGAAATTAAGTAGAGTT
* *
17681 AAGGACTTGATTCCAAGGAA-GAGAATCAAGTA-A--T
1 AAGGACTTAATTCCAAGGAAGGA-AATTAAGTAGAGTT
* *
17715 --GGACTTAATTTCAAGGGAGGAAATTAAGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
*
17750 AAGGACTTAATTCCAAGGAAGGGAATTAAGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
* *
17787 AAGGACTTAATTCCAAGGAAGGGAATTACGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
*
17824 AAGGACTTAATTTCAAGGAAGGAAATTAAGT--AG--
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
* *
17857 -AGGACTTGATTCTAA-G--GG-AATTAAGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
* *
17889 AAGGACTTAATTTCAAGCAAGGAAATTAAGTCA-AGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGT-AGAGTT
*
17926 AGGGACTTAATTC
1 AAGGACTTAATTC
17939 AGGGTAATTA
Statistics
Matches: 217, Mismatches: 24, Indels: 35
0.79 0.09 0.13
Matches are distributed among these distances:
28 8 0.04
29 2 0.01
30 2 0.01
31 1 0.00
32 35 0.16
33 15 0.07
35 3 0.01
36 4 0.02
37 129 0.59
38 18 0.08
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (37 bp):
AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
Found at i:17771 original size:18 final size:18
Alignment explanation
Indices: 17750--17808 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
17740 AAGTAGAGTT
17750 AAGGACTTAATTCCAAGG
1 AAGGACTTAATTCCAAGG
* * *
17768 AAGGGAATTAAGT--AGAGTT
1 AA-GGACTTAATTCCA-AG-G
17787 AAGGACTTAATTCCAAGG
1 AAGGACTTAATTCCAAGG
17805 AAGG
1 AAGG
17809 GAATTACGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 1 0.03
18 16 0.53
19 12 0.40
20 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (18 bp):
AAGGACTTAATTCCAAGG
Found at i:18010 original size:74 final size:74
Alignment explanation
Indices: 17926--18146 Score: 245
Period size: 73 Copynumber: 3.0 Consensus size: 74
17916 AAGTCAAGTT
* *
17926 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGGGCTTAATTCAGGGTAATTAAGTAG
1 AGGGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA-GACTTAATTCAGGGTAATTAAGTAG
*
17991 CGTCAATAAA
65 AGTCAATAAA
* * *
18001 AGGG-CTTAATTCAGGGTAATTAAGTAGAGTTAATAAAAGACTTAATTTAGGGTAATTAAGTGGA
1 AGGGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAAGACTTAATTCAGGGTAATTAAGTAGA
18065 GTCAAT-AA
66 GTCAATAAA
* * ** ** *
18073 A-GAACTTAATCTAAAAAG-AGATTAAGTA-AAACAATAAAAGACTTAATTTAGGGTAATTAAGT
1 AGGGACTTAAT-T-CAGGGTA-ATTAAGTAGAGTCAATAAAAGACTTAATTCAGGGTAATTAAGT
*
18135 GGAGTCAATAAA
63 AGAGTCAATAAA
18147 GAACTTAATC
Statistics
Matches: 128, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
71 1 0.01
72 9 0.07
73 70 0.55
74 44 0.34
75 4 0.03
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (74 bp):
AGGGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAAGACTTAATTCAGGGTAATTAAGTAGA
GTCAATAAA
Found at i:18053 original size:36 final size:36
Alignment explanation
Indices: 17929--18155 Score: 237
Period size: 37 Copynumber: 6.2 Consensus size: 36
17919 TCAAGTTAGG
*
17929 GACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* *
17965 GGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAAA
1 -GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* *
18002 GGGCTTAATTCAGGGTAATTAAGTAGAGTTAATAAAA
1 -GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* *
18039 GACTTAATTTAGGGTAATTAAGTGGAGTCAAT-AAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* ** **
18074 GAACTTAATCTAAAAAG-AGATTAAGTA-AAACAATAAAA
1 G-ACTTAAT-T-CAGGGTA-ATTAAGTAGAGTCAATAAAA
* *
18112 GACTTAATTTAGGGTAATTAAGTGGAGTCAAT-AAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
18147 GAACTTAAT
1 G-ACTTAAT
18156 CTAAAAGAGA
Statistics
Matches: 163, Mismatches: 19, Indels: 17
0.82 0.10 0.09
Matches are distributed among these distances:
35 17 0.10
36 49 0.30
37 84 0.52
38 13 0.08
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (36 bp):
GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
Found at i:18180 original size:36 final size:36
Alignment explanation
Indices: 18067--18182 Score: 103
Period size: 36 Copynumber: 3.2 Consensus size: 36
18057 TAAGTGGAGT
18067 CAATAAAGAACTTAATCTAAAAAGAGATTAAGTAAAA
1 CAATAAAGAACTTAATCT-AAAAGAGATTAAGTAAAA
* ** * **
18104 CAATAAA-AGACTTAAT-TTAGGGTA-ATTAAGTGGAGT
1 CAATAAAGA-ACTTAATCTAAAAG-AGATTAAGT-AAAA
* *
18140 CAATAAAGAACTTAATCTAAAAGAGATTAAATCAAA
1 CAATAAAGAACTTAATCTAAAAGAGATTAAGTAAAA
18176 CAATAAA
1 CAATAAA
18183 AGGGCTTGAT
Statistics
Matches: 60, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
35 9 0.15
36 27 0.45
37 24 0.40
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (36 bp):
CAATAAAGAACTTAATCTAAAAGAGATTAAGTAAAA
Found at i:18195 original size:73 final size:73
Alignment explanation
Indices: 18032--18184 Score: 281
Period size: 73 Copynumber: 2.1 Consensus size: 73
18022 AAGTAGAGTT
18032 AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
1 AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
*
18097 AGTAAAAC
66 AATAAAAC
18105 AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCT-AAAAGAGATTA
1 AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
*
18169 AATCAAAC
66 AATAAAAC
18177 AATAAAAG
1 AATAAAAG
18185 GGCTTGATTT
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
72 25 0.32
73 53 0.68
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (73 bp):
AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
AATAAAAC
Done.