Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019196.1 Corchorus olitorius cultivar O-4 contig19229, 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: 82811
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:8521 original size:2 final size:2
Alignment explanation
Indices: 8503--8557 Score: 83
Period size: 2 Copynumber: 27.0 Consensus size: 2
8493 GTACTTTTTA
* *
8503 AT AT AGT AT AG AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8546 AT AT AT AT AT AT
1 AT AT AT AT AT AT
8558 TTACAAGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13113 original size:11 final size:11
Alignment explanation
Indices: 13097--13121 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13087 TATAATAAGT
13097 GATGGAAAGAA
1 GATGGAAAGAA
13108 GATGGAAAGAA
1 GATGGAAAGAA
13119 GAT
1 GAT
13122 AAAAACAATG
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:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (11 bp):
GATGGAAAGAA
Found at i:18195 original size:123 final size:123
Alignment explanation
Indices: 17976--18206 Score: 444
Period size: 123 Copynumber: 1.9 Consensus size: 123
17966 CTAAAGTCAG
17976 TAAAAGTTCTAATTTTATATTGAGTACATAATTTCAAACTCTATAGTTCACTTTACAATAAATAA
1 TAAAAGTTCTAATTTTATATTGAGTACATAATTTCAAACTCTATAGTTCACTTTACAATAAATAA
18041 AAATGTGAAGCAAACAAACTCAGAAGAAGAAATAGAAGAATGAACAGGAACTCTGGTA
66 AAATGTGAAGCAAACAAACTCAGAAGAAGAAATAGAAGAATGAACAGGAACTCTGGTA
**
18099 TAAAAGTTCTAATTTTATATTGAGTACATAATTTCAAACTCTATAGTTCACTTTACAATGCATAA
1 TAAAAGTTCTAATTTTATATTGAGTACATAATTTCAAACTCTATAGTTCACTTTACAATAAATAA
18164 AAATGTGAAGCAAACAAACTCAGAAGAAGAAATAGAAGAATGA
66 AAATGTGAAGCAAACAAACTCAGAAGAAGAAATAGAAGAATGA
18207 GCAGAAATTC
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 106 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.28
Consensus pattern (123 bp):
TAAAAGTTCTAATTTTATATTGAGTACATAATTTCAAACTCTATAGTTCACTTTACAATAAATAA
AAATGTGAAGCAAACAAACTCAGAAGAAGAAATAGAAGAATGAACAGGAACTCTGGTA
Found at i:20349 original size:2 final size:2
Alignment explanation
Indices: 20342--20371 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20332 TAACGCTCAG
20342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20372 CTACTTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33810 original size:44 final size:44
Alignment explanation
Indices: 33761--33847 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
33751 ATCTGTAGAG
33761 TACCTAATTTGATATGTTCAATATTATCTCATCTATACAGTACA
1 TACCTAATTTGATATGTTCAATATTATCTCATCTATACAGTACA
*
33805 TACCTAATTTGATATGTTCAATATTATCTCATTTATACAGTAC
1 TACCTAATTTGATATGTTCAATATTATCTCATCTATACAGTAC
33848 CTAAACAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (44 bp):
TACCTAATTTGATATGTTCAATATTATCTCATCTATACAGTACA
Found at i:54887 original size:68 final size:67
Alignment explanation
Indices: 54770--54906 Score: 220
Period size: 68 Copynumber: 2.0 Consensus size: 67
54760 AGGCCCATGG
*
54770 AAACTCGTAAATAGTCCAATAGAATCAAGACATGTGTTAAAGGGAAAAAAAGACAATTATCCGAT
1 AAACTCGTAAATAGTCCAATAGAATCAAGACACGTGTTAAAGGG-AAAAAAGACAATTATCCGAT
54835 CTT
65 CTT
* * * *
54838 AAACTCGTAAATAGTCCAATAGAATCAATACACGTGTTGACGGGCAAAAAGACAATTATCCGATC
1 AAACTCGTAAATAGTCCAATAGAATCAAGACACGTGTTAAAGGGAAAAAAGACAATTATCCGATC
54903 TT
66 TT
54905 AA
1 AA
54907 TCCTTTCGGA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
67 24 0.38
68 40 0.62
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (67 bp):
AAACTCGTAAATAGTCCAATAGAATCAAGACACGTGTTAAAGGGAAAAAAGACAATTATCCGATC
TT
Found at i:62266 original size:19 final size:19
Alignment explanation
Indices: 62242--62278 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
62232 CACCACACGA
62242 TTATCCAGCTCAATCTTAG
1 TTATCCAGCTCAATCTTAG
62261 TTATCCAGCTCAATCTTA
1 TTATCCAGCTCAATCTTA
62279 ACTAGTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (19 bp):
TTATCCAGCTCAATCTTAG
Found at i:62467 original size:2 final size:2
Alignment explanation
Indices: 62460--62497 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
62450 TATATCTTTA
62460 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62498 GAAATGATCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63638 original size:32 final size:32
Alignment explanation
Indices: 63602--63682 Score: 162
Period size: 32 Copynumber: 2.5 Consensus size: 32
63592 TTTTCTATTT
63602 AAGATTTGATGTTTATTTATTTCAAAAAAAAA
1 AAGATTTGATGTTTATTTATTTCAAAAAAAAA
63634 AAGATTTGATGTTTATTTATTTCAAAAAAAAA
1 AAGATTTGATGTTTATTTATTTCAAAAAAAAA
63666 AAGATTTGATGTTTATT
1 AAGATTTGATGTTTATT
63683 AGTAAATTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (32 bp):
AAGATTTGATGTTTATTTATTTCAAAAAAAAA
Found at i:77206 original size:18 final size:18
Alignment explanation
Indices: 77171--77207 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
77161 TAACTGAGGA
**
77171 GTGACGTGGAGGTGGGTG
1 GTGACGTGGAGGAAGGTG
77189 GTGACGTGGAGGAAGGTG
1 GTGACGTGGAGGAAGGTG
77207 G
1 G
77208 GGATGCGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.05, G:0.59, T:0.19
Consensus pattern (18 bp):
GTGACGTGGAGGAAGGTG
Found at i:80466 original size:21 final size:19
Alignment explanation
Indices: 80442--80499 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
80432 GCTGCTCTAA
80442 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
80463 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
80482 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
80500 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:80607 original size:18 final size:18
Alignment explanation
Indices: 80581--80616 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
80571 GTAGTTTGTG
*
80581 GTAGGTTTTTTTAGATGA
1 GTAGGTTTTTTTAAATGA
*
80599 GTAGTTTTTTTTAAATGA
1 GTAGGTTTTTTTAAATGA
80617 TATAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (18 bp):
GTAGGTTTTTTTAAATGA
Found at i:82786 original size:1 final size:1
Alignment explanation
Indices: 82780--82811 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
82770 GTACTATAGG
82780 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.