Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014614.1 Corchorus olitorius cultivar O-4 contig14647, 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: 44316
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:380 original size:31 final size:31
Alignment explanation
Indices: 316--380 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
306 AAAAAGATGA
* *
316 TCAATTTAGTCTATATATTCAAAAGTTTGAG
1 TCAATTTAGTCAATATACTCAAAAGTTTGAG
* *
347 TCAATTTAGTCAATGTACTCATAAGATTT-AG
1 TCAATTTAGTCAATATACTCAAAAG-TTTGAG
378 TCA
1 TCA
381 CTTGAGTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (31 bp):
TCAATTTAGTCAATATACTCAAAAGTTTGAG
Found at i:479 original size:31 final size:31
Alignment explanation
Indices: 411--480 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
401 TATCGATTGG
* * * *
411 ATTAAATTGACTCAATCTTATGAGTATAGGA
1 ATTAAATTAACCCAATCTCATGAGTATAAGA
*
442 ACTAAATTAACCCAATCTCATGAGTATAAGA
1 ATTAAATTAACCCAATCTCATGAGTATAAGA
*
473 TTTAAATT
1 ATTAAATT
481 GAATACTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (31 bp):
ATTAAATTAACCCAATCTCATGAGTATAAGA
Found at i:2378 original size:2 final size:2
Alignment explanation
Indices: 2371--2397 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2361 AAAGATTAGC
2371 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 A
2398 GGAGCAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2720 original size:2 final size:2
Alignment explanation
Indices: 2713--2752 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2703 GCCGCCGACT
2713 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2753 CTTTTTTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:17590 original size:25 final size:26
Alignment explanation
Indices: 17544--17592 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
17534 TTTTGCCTCT
17544 TAAACTTCAAATCAAGACATTTTACC
1 TAAACTTCAAATCAAGACATTTTACC
* *
17570 TAAACTT-AAGTCAAGATATTTTA
1 TAAACTTCAAATCAAGACATTTTA
17593 TTTCCGAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (26 bp):
TAAACTTCAAATCAAGACATTTTACC
Found at i:21808 original size:27 final size:28
Alignment explanation
Indices: 21775--21833 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
21765 ATAAAATCAA
* * *
21775 TATTTA-GTAGTAGTTTTTTGGGAATAT
1 TATTTAGGGAGTAGTTTTTAGGGAATAC
21802 TATTTAGGGAGTAGTTTTTAGGGAATAC
1 TATTTAGGGAGTAGTTTTTAGGGAATAC
21830 TATT
1 TATT
21834 ATCTTCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.47
Consensus pattern (28 bp):
TATTTAGGGAGTAGTTTTTAGGGAATAC
Found at i:21821 original size:14 final size:14
Alignment explanation
Indices: 21783--21825 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
21773 AATATTTAGT
*
21783 AGTAGTTTTTTGGG
1 AGTAGTTTTTAGGG
*
21797 AATA-TTATTTAGGG
1 AGTAGTT-TTTAGGG
21811 AGTAGTTTTTAGGG
1 AGTAGTTTTTAGGG
21825 A
1 A
21826 ATACTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.08
14 20 0.83
15 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (14 bp):
AGTAGTTTTTAGGG
Found at i:25569 original size:13 final size:13
Alignment explanation
Indices: 25551--25586 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
25541 GTTAGTTGAG
25551 TTTGTTGAGTCAA
1 TTTGTTGAGTCAA
*
25564 TTTGTTGAGTCAG
1 TTTGTTGAGTCAA
25577 TTTGTTGAGT
1 TTTGTTGAGT
25587 TTGAGTCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (13 bp):
TTTGTTGAGTCAA
Found at i:26375 original size:15 final size:16
Alignment explanation
Indices: 26345--26386 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
26335 ATTTTAAAGT
26345 AAAAGGAGAAAAGAAA
1 AAAAGGAGAAAAGAAA
*
26361 AAAAGGA-AAATGAAA
1 AAAAGGAGAAAAGAAA
26376 ATAAAGAGAGA
1 A-AAAG-GAGA
26387 TATGGGTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 2 0.09
18 1 0.05
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (16 bp):
AAAAGGAGAAAAGAAA
Found at i:42832 original size:21 final size:21
Alignment explanation
Indices: 42806--42845 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42796 ATGAGATTAC
*
42806 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTATGT
42827 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
42846 TAGAGCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (21 bp):
ACTGTACAGATGAGATTATGT
Found at i:43884 original size:82 final size:82
Alignment explanation
Indices: 43747--43988 Score: 432
Period size: 82 Copynumber: 3.0 Consensus size: 82
43737 CAGGGTAAAC
*
43747 CGTCAATTTATTTTGGGATTTACGGAGTTTCACCTGCGGGTTTTTTGGAATTTACAGATCACCTA
1 CGTCAATTTATTTTGGGATTTACGGAGTTTCACCTGCGGGTTTTTTGGAATTTACAAATCACCTA
43812 CCAAATGAGAGA-CTGCT
66 CCAAATGAGAGATC-GCT
*
43829 CGTCAATTTATTTTGGGATTTACGGAGTTTCACCTGCGGGTTTTTTGGAATTTACATATCACCTA
1 CGTCAATTTATTTTGGGATTTACGGAGTTTCACCTGCGGGTTTTTTGGAATTTACAAATCACCTA
43894 CCAAATGAGAGATCGCT
66 CCAAATGAGAGATCGCT
* *
43911 CGTCAATTTATTTTGGGATTTACGGACTTTCACCTGCGGGTTTTTTGGAATTTACAAATCACGTA
1 CGTCAATTTATTTTGGGATTTACGGAGTTTCACCTGCGGGTTTTTTGGAATTTACAAATCACCTA
43976 CCAAATGAGAGAT
66 CCAAATGAGAGAT
43989 TGCAGTCAGC
Statistics
Matches: 155, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
82 154 0.99
83 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (82 bp):
CGTCAATTTATTTTGGGATTTACGGAGTTTCACCTGCGGGTTTTTTGGAATTTACAAATCACCTA
CCAAATGAGAGATCGCT
Done.