Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015328.1 Corchorus olitorius cultivar O-4 contig15361, 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: 41701
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3766 original size:19 final size:19
Alignment explanation
Indices: 3742--3778 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3732 TCTAAGGAGA
3742 AACCCTTAAGCAACGTCTT
1 AACCCTTAAGCAACGTCTT
*
3761 AACCCTTAAGCAAGGTCT
1 AACCCTTAAGCAACGTCT
3779 CAAAAGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (19 bp):
AACCCTTAAGCAACGTCTT
Found at i:6045 original size:24 final size:26
Alignment explanation
Indices: 6018--6069 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
6008 GACCTATTCG
6018 GCCC-AAAAA-AACAAACTGGACCTA
1 GCCCAAAAAAGAACAAACTGGACCTA
6042 GCCCAAAAAAGAACAAACTGGACCTA
1 GCCCAAAAAAGAACAAACTGGACCTA
6068 GC
1 GC
6070 TCAATAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 4 0.15
25 5 0.19
26 17 0.65
ACGTcount: A:0.48, C:0.29, G:0.15, T:0.08
Consensus pattern (26 bp):
GCCCAAAAAAGAACAAACTGGACCTA
Found at i:10778 original size:29 final size:29
Alignment explanation
Indices: 10718--10784 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
10708 ACAAAAAATG
***
10718 GCCAAATAAGCCCCTGAACTCTAATTGCA
1 GCCAAATAAGCCCCTGAACTCTAATAAAA
10747 GCCAAATAAGCCCCTGAACTCTTAA-AAAA
1 GCCAAATAAGCCCCTGAACTC-TAATAAAA
10776 GCCAAATAA
1 GCCAAATAA
10785 ACCTTTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 31 0.91
30 3 0.09
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (29 bp):
GCCAAATAAGCCCCTGAACTCTAATAAAA
Found at i:12509 original size:2 final size:2
Alignment explanation
Indices: 12502--12531 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12492 CAATTAAGTA
*
12502 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12532 TCATATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12986 original size:16 final size:16
Alignment explanation
Indices: 12965--13003 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
12955 AATAATGATA
12965 TAATTAAACATCACTC
1 TAATTAAACATCACTC
*
12981 TAATTAAACATCACTT
1 TAATTAAACATCACTC
12997 TAATTAA
1 TAATTAA
13004 CCGTCATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATTAAACATCACTC
Found at i:17593 original size:60 final size:60
Alignment explanation
Indices: 17524--17648 Score: 198
Period size: 60 Copynumber: 2.1 Consensus size: 60
17514 AATATTTACT
* * *
17524 AAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGTCAAATAA-GAGCCTAACGTTATCG
1 AAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGCCAAATAAGGA-CCTAACGTTATCG
*
17584 AAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGCCAAATAAGGACTTAACGTTATCG
1 AAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGCCAAATAAGGACCTAACGTTATCG
17644 AAAAT
1 AAAAT
17649 AAGGGCCTGA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 58 0.97
61 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGCCAAATAAGGACCTAACGTTATCG
Found at i:20312 original size:51 final size:51
Alignment explanation
Indices: 20236--20332 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 51
20226 AGACCAGAAC
*
20236 TTGTATTCGACCCCATAAAATCATTACTACTTGAACCAAAACCACTTGGTG
1 TTGTATTCGACCCCATAAAATCATTACTACTCGAACCAAAACCACTTGGTG
*
20287 TTGTATTCGACCCCATAAAATCATTATTACTCGAACCAAAACCACT
1 TTGTATTCGACCCCATAAAATCATTACTACTCGAACCAAAACCACT
20333 AGATGGAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.29
Consensus pattern (51 bp):
TTGTATTCGACCCCATAAAATCATTACTACTCGAACCAAAACCACTTGGTG
Found at i:26037 original size:28 final size:28
Alignment explanation
Indices: 25994--26055 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
25984 GGGGCTACCC
*
25994 TAAACTAAAATCGAGATACTTTGCCCCA
1 TAAACTAAAATCGAGACACTTTGCCCCA
* * *
26022 TAAATTAAAATTGAGACATTTTGCCCCA
1 TAAACTAAAATCGAGACACTTTGCCCCA
26050 TAAACT
1 TAAACT
26056 TTCCAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (28 bp):
TAAACTAAAATCGAGACACTTTGCCCCA
Found at i:27097 original size:62 final size:62
Alignment explanation
Indices: 27000--27122 Score: 237
Period size: 62 Copynumber: 2.0 Consensus size: 62
26990 AGCATAAAGG
*
27000 TTAAAGTCTTCTCAAGGAATGCGTTCTAACAAGATCGGCCTTGTATTCTCACCCTTCATGAT
1 TTAAAATCTTCTCAAGGAATGCGTTCTAACAAGATCGGCCTTGTATTCTCACCCTTCATGAT
27062 TTAAAATCTTCTCAAGGAATGCGTTCTAACAAGATCGGCCTTGTATTCTCACCCTTCATGA
1 TTAAAATCTTCTCAAGGAATGCGTTCTAACAAGATCGGCCTTGTATTCTCACCCTTCATGA
27123 ACAAAGACCG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (62 bp):
TTAAAATCTTCTCAAGGAATGCGTTCTAACAAGATCGGCCTTGTATTCTCACCCTTCATGAT
Found at i:27200 original size:18 final size:18
Alignment explanation
Indices: 27177--27230 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
27167 CATGTTCACG
27177 TTCATGTATATAACTGAA
1 TTCATGTATATAACTGAA
27195 TTCATGTATATAACTGAA
1 TTCATGTATATAACTGAA
27213 TTCATGTATATAACTGAA
1 TTCATGTATATAACTGAA
27231 ACTTGTATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
TTCATGTATATAACTGAA
Found at i:41191 original size:4 final size:4
Alignment explanation
Indices: 41182--41227 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
41172 CTGTAATAAT
41182 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
41228 GATAGAAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Done.