Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013712.1 Corchorus olitorius cultivar O-4 contig13745, 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: 35644
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:9151 original size:47 final size:48
Alignment explanation
Indices: 9071--9165 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 48
9061 TAATCTTTTA
9071 TTTGTCCAACTTTGCCCCCTGAAGTATGAAAATAAGGACAATTTGCGT
1 TTTGTCCAACTTTGCCCCCTGAAGTATGAAAATAAGGACAATTTGCGT
*
9119 TTTGTCCAACTTTG-CCTCTGAAGTATGAAAATAAGGACAATTTGCGT
1 TTTGTCCAACTTTGCCCCCTGAAGTATGAAAATAAGGACAATTTGCGT
9166 GCACGTGACT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 32 0.70
48 14 0.30
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (48 bp):
TTTGTCCAACTTTGCCCCCTGAAGTATGAAAATAAGGACAATTTGCGT
Found at i:13216 original size:2 final size:2
Alignment explanation
Indices: 13209--13239 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
13199 GTTTTTATTA
13209 GT GT GT GT GT GT GT GT GT GT GT GT AGT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT -GT GT GT
13240 AAATGCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.03, C:0.00, G:0.48, T:0.48
Consensus pattern (2 bp):
GT
Found at i:21899 original size:29 final size:31
Alignment explanation
Indices: 21874--21941 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
21864 ATGCAATTTG
*
21874 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTCACGAAAAGCAAGCAATTAA
* *
21903 GAATATAACGTCACGAAAAGCGAGCAATTAA
1 GGATATAACGTCACGAAAAGCAAGCAATTAA
21934 GGATATAA
1 GGATATAA
21942 TCCGTTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 12 0.36
30 4 0.12
31 17 0.52
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.19
Consensus pattern (31 bp):
GGATATAACGTCACGAAAAGCAAGCAATTAA
Found at i:22096 original size:31 final size:31
Alignment explanation
Indices: 22061--22139 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
22051 CTAACTGATT
**
22061 ATATCCTTAATTGCTTGAAATCGAAAACCTC
1 ATATCCTTAATTGCTTGAAATAAAAAACCTC
* *
22092 ATATCCTTAATTGCTTGAAATAAAAAACGTT
1 ATATCCTTAATTGCTTGAAATAAAAAACCTC
*
22123 ATATCTTTAATTGCTTG
1 ATATCCTTAATTGCTTG
22140 TTTTGTAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAAAAAACCTC
Found at i:23045 original size:16 final size:16
Alignment explanation
Indices: 23026--23056 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
23016 ATATTCTAAG
23026 AATACATTTTTCTACT
1 AATACATTTTTCTACT
23042 AATACATTTTTCTAC
1 AATACATTTTTCTAC
23057 CAAGCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (16 bp):
AATACATTTTTCTACT
Found at i:23134 original size:16 final size:16
Alignment explanation
Indices: 23113--23158 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
23103 CCTTATATAC
23113 AATAAAAAGTTATTTA
1 AATAAAAAGTTATTTA
* *
23129 AATAAAATGTTTTTTA
1 AATAAAAAGTTATTTA
*
23145 AA-AAAAAATTATTT
1 AATAAAAAGTTATTT
23159 TCTTCTCAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
AATAAAAAGTTATTTA
Found at i:23697 original size:31 final size:31
Alignment explanation
Indices: 23659--23722 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
23649 CAATGGCCGT
**
23659 AAGCAATTAAGGATATAACGTTTTTTATTTC
1 AAGCAATTAAGGATATAACGTTTTCGATTTC
*
23690 AAGCAATTAAGGATATGACGTTTTCGATTTC
1 AAGCAATTAAGGATATAACGTTTTCGATTTC
23721 AA
1 AA
23723 AGGATATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (31 bp):
AAGCAATTAAGGATATAACGTTTTCGATTTC
Found at i:26973 original size:15 final size:15
Alignment explanation
Indices: 26937--26990 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
26927 CTATTCTAAA
26937 ACCCCTCCCAAACCCTC
1 ACCCCTCCC-AACCC-C
*
26954 A-CCCTCCCTACCCC
1 ACCCCTCCCAACCCC
*
26968 ACCCCTCCCCACCCC
1 ACCCCTCCCAACCCC
26983 ACCCCTCC
1 ACCCCTCC
26991 TCATTTGATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 2 0.06
15 24 0.71
16 7 0.21
17 1 0.03
ACGTcount: A:0.17, C:0.72, G:0.00, T:0.11
Consensus pattern (15 bp):
ACCCCTCCCAACCCC
Found at i:28214 original size:2 final size:2
Alignment explanation
Indices: 28176--28202 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28166 AAGTAAATTA
28176 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
28203 CCATAATATA
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
Done.