Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010031.1 Corchorus capsularis cultivar CVL-1 contig10052, 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: 17762
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1206 original size:34 final size:34
Alignment explanation
Indices: 1168--1272 Score: 180
Period size: 34 Copynumber: 3.2 Consensus size: 34
1158 TAACCCGTTA
1168 GCAGGGTCTTCCAGTTATTATCACAACCCACTGG
1 GCAGGGTCTTCCAGTTATTATCACAACCCACTGG
*
1202 GCAGGGTCTTCCAGTTATTTTCACAACCCACTGG
1 GCAGGGTCTTCCAGTTATTATCACAACCCACTGG
1236 GCAGGGTCTTCCAGTTATTAT---AACCCACTGG
1 GCAGGGTCTTCCAGTTATTATCACAACCCACTGG
1267 GCAGGG
1 GCAGGG
1273 CCGATGAAAC
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
31 16 0.23
34 53 0.77
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.27
Consensus pattern (34 bp):
GCAGGGTCTTCCAGTTATTATCACAACCCACTGG
Found at i:1646 original size:20 final size:20
Alignment explanation
Indices: 1603--1646 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1593 TTACCTGTCT
*
1603 CCAACTAACACGGCCTTTCA
1 CCAACTAACACGGCCTTCCA
* *
1623 CCAACTAATACGGCCTTCCC
1 CCAACTAACACGGCCTTCCA
1643 CCAA
1 CCAA
1647 ACTACTTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.43, G:0.09, T:0.18
Consensus pattern (20 bp):
CCAACTAACACGGCCTTCCA
Found at i:3056 original size:21 final size:21
Alignment explanation
Indices: 3032--3074 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3022 TTGACTTGCG
3032 TGTAGTTCCTGTAATTGAGTA
1 TGTAGTTCCTGTAATTGAGTA
3053 TGTAGTTCCTGTAATTGAGTA
1 TGTAGTTCCTGTAATTGAGTA
3074 T
1 T
3075 TGAAAGAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44
Consensus pattern (21 bp):
TGTAGTTCCTGTAATTGAGTA
Found at i:8116 original size:40 final size:40
Alignment explanation
Indices: 8065--8142 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
8055 TTATAATTAT
* *
8065 GGGTTATATCTGGATTTAATGTCTTACCTTAATTATTAGG
1 GGGTTAAATCTGGATTTAATGTATTACCTTAATTATTAGG
* **
8105 GGGTTAAATCTGGATTTAATTTATTTTCTTAATTATTA
1 GGGTTAAATCTGGATTTAATGTATTACCTTAATTATTA
8143 CTATAAGAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.49
Consensus pattern (40 bp):
GGGTTAAATCTGGATTTAATGTATTACCTTAATTATTAGG
Found at i:8264 original size:2 final size:2
Alignment explanation
Indices: 8257--8283 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8247 TTTATTTATG
8257 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
8284 AATCAGTTTC
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:12532 original size:17 final size:17
Alignment explanation
Indices: 12510--12542 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12500 ATTAATTATT
12510 GTTAATACTTTTGTGTG
1 GTTAATACTTTTGTGTG
12527 GTTAATACTTTTGTGT
1 GTTAATACTTTTGTGT
12543 AATTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.21, T:0.55
Consensus pattern (17 bp):
GTTAATACTTTTGTGTG
Found at i:12548 original size:17 final size:17
Alignment explanation
Indices: 12511--12562 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
12501 TTAATTATTG
**
12511 TTAATACTTTTGTGTGG
1 TTAATACTTTTGTGTAA
12528 TTAATACTTTTGTGTAA
1 TTAATACTTTTGTGTAA
12545 TTAATA--TTTG-GTAA
1 TTAATACTTTTGTGTAA
12559 TTAA
1 TTAA
12563 ATTTTACAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 8 0.24
15 4 0.12
17 21 0.64
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.52
Consensus pattern (17 bp):
TTAATACTTTTGTGTAA
Found at i:15463 original size:44 final size:40
Alignment explanation
Indices: 15397--15480 Score: 107
Period size: 44 Copynumber: 2.0 Consensus size: 40
15387 TATGTTTAAA
15397 ATCATATATATAAAGTCAAGGCAAA-TAAGCAAACCTGAGC
1 ATCATATATATAAAGTCAAGGCAAAGT-AGCAAACCTGAGC
*
15437 ATCATATATATAAAGTCAAACAAGGCAAAGTAGCAAACTTGAGC
1 ATCATATATATAAAGT----CAAGGCAAAGTAGCAAACCTGAGC
15481 GGCAGTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
40 16 0.42
44 21 0.55
45 1 0.03
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (40 bp):
ATCATATATATAAAGTCAAGGCAAAGTAGCAAACCTGAGC
Done.