Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023917.1 Corchorus olitorius cultivar O-4 contig23950, 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: 18517
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:4046 original size:77 final size:77
Alignment explanation
Indices: 3963--4163 Score: 377
Period size: 77 Copynumber: 2.6 Consensus size: 77
3953 TCCTAGACAT
**
3963 TATACCATGAATAAACTACATACAAACCAAATACACAAATAACATAAATAAACTACAAACTAAAC
1 TATACCACAAATAAACTACATACAAACCAAATACACAAATAACATAAATAAACTACAAACTAAAC
4028 TCATATTCAAAC
66 TCATATTCAAAC
4040 TATACCACAAATAAACTACATACAAACCAAATACACAAATAACATAAATAAACTACAAACTAAAC
1 TATACCACAAATAAACTACATACAAACCAAATACACAAATAACATAAATAAACTACAAACTAAAC
4105 TCATATTCAAAC
66 TCATATTCAAAC
4117 TATACCACAAATAAACTACATACAAACCAAATACACAAATAA-ATAAA
1 TATACCACAAATAAACTACATACAAACCAAATACACAAATAACATAAA
4164 CTATAAACTA
Statistics
Matches: 122, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
76 5 0.04
77 117 0.96
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (77 bp):
TATACCACAAATAAACTACATACAAACCAAATACACAAATAACATAAATAAACTACAAACTAAAC
TCATATTCAAAC
Found at i:4058 original size:40 final size:40
Alignment explanation
Indices: 4008--4136 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
3998 CAAATAACAT
4008 AAATAAACTACAAACTAAACTCATATTCAAACTATACCAC
1 AAATAAACTACAAACTAAACTCATATTCAAACTATACCAC
* * * * *
4048 AAATAAACTACATAC-AAAC-CAAATACACAA--ATAACAT
1 AAATAAACTACAAACTAAACTCATATTCA-AACTATACCAC
4085 AAATAAACTACAAACTAAACTCATATTCAAACTATACCAC
1 AAATAAACTACAAACTAAACTCATATTCAAACTATACCAC
4125 AAATAAACTACA
1 AAATAAACTACA
4137 TACAAACCAA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
37 19 0.26
38 12 0.16
39 12 0.16
40 31 0.42
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (40 bp):
AAATAAACTACAAACTAAACTCATATTCAAACTATACCAC
Found at i:4076 original size:28 final size:27
Alignment explanation
Indices: 4045--4159 Score: 86
Period size: 28 Copynumber: 4.4 Consensus size: 27
4035 CAAACTATAC
4045 CACAAATAAACTACATACAAACCAAATA
1 CACAAATAAACTACATACAAA-CAAATA
*
4073 CACAAAT--A--ACATA-AATA-AACTA
1 CACAAATAAACTACATACAA-ACAAATA
* *
4095 CA-AACTAAACT-CATATTCAAAC-TATA
1 CACAAATAAACTACATA--CAAACAAATA
4121 CCACAAATAAACTACATACAAACCAAATA
1 -CACAAATAAACTACATACAAA-CAAATA
4150 CACAAATAAA
1 CACAAATAAA
4160 TAAACTATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 28
0.66 0.06 0.28
Matches are distributed among these distances:
21 3 0.04
22 6 0.09
23 3 0.04
24 10 0.15
26 4 0.06
27 8 0.12
28 26 0.39
29 7 0.10
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.17
Consensus pattern (27 bp):
CACAAATAAACTACATACAAACAAATA
Found at i:11931 original size:42 final size:42
Alignment explanation
Indices: 11879--11971 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
11869 CTCTAACGAT
*
11879 GGAGGCAAATCAGGATCTCAATCAGAGACGGTATCTCTCTTG
1 GGAGCCAAATCAGGATCTCAATCAGAGACGGTATCTCTCTTG
*
11921 GGATCCAAATCAGGATCTCAATCAGAGACGGTATCTCTCTTG
1 GGAGCCAAATCAGGATCTCAATCAGAGACGGTATCTCTCTTG
11963 GGAGCCAAA
1 GGAGCCAAA
11972 GCCGATTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (42 bp):
GGAGCCAAATCAGGATCTCAATCAGAGACGGTATCTCTCTTG
Found at i:15906 original size:19 final size:18
Alignment explanation
Indices: 15882--15917 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15872 TGAAGACTTA
15882 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
15901 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
15918 ATTATCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:18181 original size:76 final size:76
Alignment explanation
Indices: 18044--18195 Score: 182
Period size: 76 Copynumber: 2.0 Consensus size: 76
18034 AGAAGGGCCC
* * * *
18044 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCTTGAGGACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCACGTGGTTTGCCTGAGCACCCAGAT
18109 GGGCGGTGTCA
66 GGGCGGTGTCA
* * * * *
18120 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAGACCCACGT-GTTTCGCCTGATCACCCAG
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAACACCCACGTGGTTT-GCCTGAGCACCCAG
*
18183 ATGGGCTGTGTCA
64 ATGGGCGGTGTCA
18196 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
75 4 0.06
76 56 0.88
77 4 0.06
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCACGTGGTTTGCCTGAGCACCCAGAT
GGGCGGTGTCA
Done.