Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013878.1 Corchorus capsularis cultivar CVL-1 contig13899, 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: 23003
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:150 original size:2 final size:2
Alignment explanation
Indices: 143--176 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
133 TCAAATTTAC
143 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
177 TATTTTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:367 original size:72 final size:74
Alignment explanation
Indices: 260--414 Score: 242
Period size: 73 Copynumber: 2.1 Consensus size: 74
250 TGGTCTTTTC
* **
260 ACACTTTTCGGGTAACTAAAAAGCCCCTCTATGAGTTT-CCTTATTCCTTTTCCTTCTACCATTT
1 ACACTTTTCGGATAACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCATTT
324 TTCGTAATT
66 TTCGTAATT
* *
333 ACACTTTTCGGATGACT-AAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATAACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCATTT
397 TTCGTAATT
66 TTCGTAATT
*
406 ACACATTTC
1 ACACTTTTC
415 CCTTCCTTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
72 20 0.27
73 55 0.73
ACGTcount: A:0.21, C:0.29, G:0.09, T:0.41
Consensus pattern (74 bp):
ACACTTTTCGGATAACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCATTT
TTCGTAATT
Found at i:4276 original size:33 final size:33
Alignment explanation
Indices: 4172--4264 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
4162 TGACCCGTGT
4172 CGCCCCAGGAGGGCGGCTTACCATGGCTCAAGC
1 CGCCCCAGGAGGGCGGCTTACCATGGCTCAAGC
*
4205 CGCCCCAGGAGGGTGGCTTACCATGGCTCAAGC
1 CGCCCCAGGAGGGCGGCTTACCATGGCTCAAGC
4238 CGCCCCAGTG-GGGCGGCTTCACCATGG
1 CGCCCCAG-GAGGGCGGCTT-ACCATGG
4265 GCAGGCCGCC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
33 48 0.86
34 8 0.14
ACGTcount: A:0.16, C:0.35, G:0.34, T:0.14
Consensus pattern (33 bp):
CGCCCCAGGAGGGCGGCTTACCATGGCTCAAGC
Found at i:4402 original size:33 final size:33
Alignment explanation
Indices: 4360--4441 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
4350 GTCTAGCCGC
* *
4360 CCTAGTGGGGCGGCTCCGCCATGGCTGAGCCAT
1 CCTAGTGGGGAGGCTCCGCCATGGCGGAGCCAT
* *
4393 CCTAGTGGGGAGGCTCCGCCGTGGCGGAGCCGT
1 CCTAGTGGGGAGGCTCCGCCATGGCGGAGCCAT
*
4426 CCTAGTGGAGAGGCTC
1 CCTAGTGGGGAGGCTC
4442 AGTGTAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.12, C:0.30, G:0.40, T:0.17
Consensus pattern (33 bp):
CCTAGTGGGGAGGCTCCGCCATGGCGGAGCCAT
Found at i:7843 original size:2 final size:2
Alignment explanation
Indices: 7836--7865 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
7826 CTTCCGTTAC
*
7836 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7866 GTATTTTTGG
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8156 original size:157 final size:159
Alignment explanation
Indices: 7969--8289 Score: 531
Period size: 158 Copynumber: 2.0 Consensus size: 159
7959 CAAAAAGTTA
* *
7969 CATTTTATATTAATTGTCATTGGATGTTTACATGTAC-TTACATTCTAAATTAAATTTTGTAACT
1 CATTCTATATTAATTGTCATTAGATGTTTACATGTACGTTACATTCTAAATTAAATTTTGTAACT
*
8033 TAATATGTTTTCCATCTTCTCAATTAATTATTTGAAATTCTAATTATGA-TTATGATATGATTAT
66 TAATATGTTTTCCATCTTCTCAATTAATTATTT-AAATTCTAATTATGACATATGATATGATTAT
*
8097 ATGCTATTA-GTGGTTACAGTTACACATTT
130 ATGCTATTATGTAGTTACAGTTACACATTT
*
8126 CATTCTATATTAATTTTCATTAGATGTTTACATGTACGTTACATTCTAAATTAAATTTTGTAACT
1 CATTCTATATTAATTGTCATTAGATGTTTACATGTACGTTACATTCTAAATTAAATTTTGTAACT
*
8191 TAATATGTTTTCCATCTTCTCAATTAATTATTTAAATTGTAATTATGACCATATGATATGATTAT
66 TAATATGTTTTCCATCTTCTCAATTAATTATTTAAATTCTAATTATGA-CATATGATATGATTAT
*
8256 ATGCTTTTATTGTAGTTACAGTTACACATTT
130 ATGCTATTA-TGTAGTTACAGTTACACATTT
8287 CAT
1 CAT
8290 AATAAACCCT
Statistics
Matches: 152, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
157 48 0.32
158 60 0.39
159 22 0.14
161 22 0.14
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (159 bp):
CATTCTATATTAATTGTCATTAGATGTTTACATGTACGTTACATTCTAAATTAAATTTTGTAACT
TAATATGTTTTCCATCTTCTCAATTAATTATTTAAATTCTAATTATGACATATGATATGATTATA
TGCTATTATGTAGTTACAGTTACACATTT
Found at i:10786 original size:83 final size:85
Alignment explanation
Indices: 10693--10859 Score: 293
Period size: 83 Copynumber: 2.0 Consensus size: 85
10683 ACAGTTTCAT
* *
10693 TCTATGAATTCTATTTCAATCATTATGTTTGATTTTGTAACGTTATAGAATA-A-ATGTTTTTCA
1 TCTATAAATTCTATTTAAATCATTATGTTTGATTTTGTAACGTTATAGAATATATATGTTTTTCA
10756 TTAAATGGAATTAATTTAGC
66 TTAAATGGAATTAATTTAGC
*
10776 TCTATAAATTCTATTTAAATCATTATGTTTGATTTTTTAACGTTATAGAATATATATGTTTTTCA
1 TCTATAAATTCTATTTAAATCATTATGTTTGATTTTGTAACGTTATAGAATATATATGTTTTTCA
10841 TTAAATGGAATTAATTTAG
66 TTAAATGGAATTAATTTAG
10860 GGCATTATTA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 49 0.62
84 1 0.01
85 29 0.37
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.49
Consensus pattern (85 bp):
TCTATAAATTCTATTTAAATCATTATGTTTGATTTTGTAACGTTATAGAATATATATGTTTTTCA
TTAAATGGAATTAATTTAGC
Found at i:13405 original size:45 final size:46
Alignment explanation
Indices: 13354--13441 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
13344 AATAGAGTAC
13354 TGGAATTACTAAAAGATCCCTACCC-AGAATTAATGAAGAGCTAGG
1 TGGAATTACTAAAAGATCCCTACCCTAGAATTAATGAAGAGCTAGG
* *
13399 TGGAATTACTAAAAGATCCCTACCCTAGGATTAATGATGAGCT
1 TGGAATTACTAAAAGATCCCTACCCTAGAATTAATGAAGAGCT
13442 GAAGAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 25 0.62
46 15 0.38
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (46 bp):
TGGAATTACTAAAAGATCCCTACCCTAGAATTAATGAAGAGCTAGG
Found at i:19356 original size:2 final size:2
Alignment explanation
Indices: 19349--19379 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19339 CTACCATAGG
19349 AT AT 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 AT AT A
19380 CTAGTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22787 original size:29 final size:29
Alignment explanation
Indices: 22729--22797 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
22719 ACCGAACCGT
****
22729 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
22758 CAAATAAGCCCCTGAACTCTTAAAAAGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
22787 CAAATAAGCCC
1 CAAATAAGCCC
22798 TATTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Done.