Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009238.1 Corchorus capsularis cultivar CVL-1 contig09259, 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: 26592
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3278 original size:25 final size:25
Alignment explanation
Indices: 3250--3305 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
3240 CTTACGTTTG
3250 GCAAACGAGCCTACGCTTGCGTTGA
1 GCAAACGAGCCTACGCTTGCGTTGA
**
3275 GCAAACGAGCCTGTGCTTGCGTTGA
1 GCAAACGAGCCTACGCTTGCGTTGA
3300 GCAAAC
1 GCAAAC
3306 ACATAGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.20
Consensus pattern (25 bp):
GCAAACGAGCCTACGCTTGCGTTGA
Found at i:4103 original size:16 final size:16
Alignment explanation
Indices: 4069--4104 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4059 TTTTTTTCAA
**
4069 TTCTCTCTCTCTTTTT
1 TTCTCTCTCTCTTCCT
4085 TTCTCTCTCTCTTCCT
1 TTCTCTCTCTCTTCCT
4101 TTCT
1 TTCT
4105 TTTCACCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTCTCTCTCTCTTCCT
Found at i:4140 original size:15 final size:15
Alignment explanation
Indices: 4120--4157 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4110 CCTTTTTTCA
*
4120 CTTTTTTTATTCTCT
1 CTTTTTTTACTCTCT
*
4135 CTTTTTTTCCTCTCT
1 CTTTTTTTACTCTCT
4150 CTTTTTTT
1 CTTTTTTT
4158 TCATTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTTTTACTCTCT
Found at i:4170 original size:55 final size:56
Alignment explanation
Indices: 4074--4179 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 56
4064 TTCAATTCTC
* *
4074 TCTCTCTTTTTTTCTCTCTCTCTTCCTTTCTTTTCACCTTTTT-TCACTTTTTTTAT
1 TCTCTCTTTTTTTCTCTCTCTCTTCCTTTCATTTCAACTTTTTAT-ACTTTTTTTAT
**
4130 TCTCTCTTTTTTTC-CTCTCTCTTTTTTTTCATTT-AACTTTTTATACTTTT
1 TCTCTCTTTTTTTCTCTCTCTC-TTCCTTTCATTTCAACTTTTTATACTTTT
4180 ATTTTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
55 20 0.45
56 24 0.55
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.67
Consensus pattern (56 bp):
TCTCTCTTTTTTTCTCTCTCTCTTCCTTTCATTTCAACTTTTTATACTTTTTTTAT
Found at i:4962 original size:7 final size:8
Alignment explanation
Indices: 4945--4970 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4935 TTTTTTCTCT
4945 AAAGAAAA
1 AAAGAAAA
4953 AAAGAAAA
1 AAAGAAAA
4961 AAAGAAAA
1 AAAGAAAA
4969 AA
1 AA
4971 TCTTCCTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:9208 original size:2 final size:2
Alignment explanation
Indices: 9201--9226 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9191 TGTAGGGTTG
9201 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9227 CTTTTAGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9418 original size:48 final size:48
Alignment explanation
Indices: 9365--9457 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
9355 TCTACAAATT
9365 ATAAAGATTTAGTAATATTTTTCAACGAATTATAAAGGTTTTAATAAA
1 ATAAAGATTTAGTAATATTTTTCAACGAATTATAAAGGTTTTAATAAA
9413 ATAAAGATTTAGTAATATTTTTCAACGAATTATAAAGGTTTTAAT
1 ATAAAGATTTAGTAATATTTTTCAACGAATTATAAAGGTTTTAAT
9458 TTTACATTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (48 bp):
ATAAAGATTTAGTAATATTTTTCAACGAATTATAAAGGTTTTAATAAA
Found at i:9562 original size:16 final size:16
Alignment explanation
Indices: 9512--9567 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
9502 TTATTTCTAC
9512 AAATTATATTGCAACT
1 AAATTATATTGCAACT
*
9528 AAATTTTCATT---AC-
1 AAATTAT-ATTGCAACT
9541 AAATTATATTGCAACT
1 AAATTATATTGCAACT
9557 AAATTATATTG
1 AAATTATATTG
9568 TTATGGTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
12 3 0.09
13 6 0.18
14 2 0.06
15 2 0.06
16 17 0.52
17 3 0.09
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (16 bp):
AAATTATATTGCAACT
Found at i:23264 original size:21 final size:21
Alignment explanation
Indices: 23235--23279 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
23225 GTGGTATTGT
*
23235 ACCATGTGAATCAAACCCAAG
1 ACCAGGTGAATCAAACCCAAG
23256 ACCAGGTGAATCAAACCCAAG
1 ACCAGGTGAATCAAACCCAAG
23277 ACC
1 ACC
23280 TAGGCACCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.31, G:0.16, T:0.11
Consensus pattern (21 bp):
ACCAGGTGAATCAAACCCAAG
Done.