Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007271.1 Corchorus capsularis cultivar CVL-1 contig07292, 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: 17805
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Found at i:5255 original size:21 final size:23
Alignment explanation
Indices: 5213--5257 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5203 AGTGGTGCTG
5213 TTATAGTTTGTTTTCCTGTCAGA
1 TTATAGTTTGTTTTCCTGTCAGA
* *
5236 TTATGGTTT-TTTTTCT-TCAGA
1 TTATAGTTTGTTTTCCTGTCAGA
5257 T
1 T
5258 CTCAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 6 0.30
23 8 0.40
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (23 bp):
TTATAGTTTGTTTTCCTGTCAGA
Found at i:5268 original size:150 final size:157
Alignment explanation
Indices: 4994--5277 Score: 440
Period size: 159 Copynumber: 1.8 Consensus size: 157
4984 TTTCCCACTA
*
4994 CAAGTTTAGATTACCATGTCTTGACATATGTGTTTTACTGAGGAATTTGGAGTGGTGCTGTTATA
1 CAAGTTTAGATTACCATGTCTTGACATATGTGTTTTACTGAGGAATTTAGAGTGGTGCTGTTATA
* * *
5059 GTTTGTTTTCCTGTCAGATTATGTTTATTTTTTTTTCTCAAGATTAGTGGTCAATATGATATTGA
66 GTTTGTTTTCCTGTCAGATTATGTGTATTTTTTTCTCTCAAG--TAGTGCTCAATATGATATTGA
5124 GGCAACTGATTGGTGGTCAGATTAGTGGT
129 GGCAACTGATTGGTGGTCAGATTAGTGGT
*
5153 CAAGTTT-GAATTACCATGTCTTGACATATGTGTTTTATTGAGGAATTTAGAGTGGTGCTGTTAT
1 CAAGTTTAG-ATTACCATGTCTTGACATATGTGTTTTACTGAGGAATTTAGAGTGGTGCTGTTAT
5217 AGTTTGTTTTCCTGTCAGATTATG-GT-TTTTTTTCT-TC-AG-A-T-CTCAATATGATATTGAG
65 AGTTTGTTTTCCTGTCAGATTATGTGTATTTTTTTCTCTCAAGTAGTGCTCAATATGATATTGAG
5275 GCA
130 GCA
5278 GCTCATTTGT
Statistics
Matches: 119, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
150 19 0.16
151 1 0.01
152 1 0.01
155 2 0.02
156 2 0.02
157 8 0.07
158 2 0.02
159 84 0.71
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.44
Consensus pattern (157 bp):
CAAGTTTAGATTACCATGTCTTGACATATGTGTTTTACTGAGGAATTTAGAGTGGTGCTGTTATA
GTTTGTTTTCCTGTCAGATTATGTGTATTTTTTTCTCTCAAGTAGTGCTCAATATGATATTGAGG
CAACTGATTGGTGGTCAGATTAGTGGT
Found at i:5294 original size:19 final size:19
Alignment explanation
Indices: 5270--5308 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5260 CAATATGATA
5270 TTGAGGCAGCTCATTTGTT
1 TTGAGGCAGCTCATTTGTT
5289 TTGAGGCAGCTCATTTGTT
1 TTGAGGCAGCTCATTTGTT
5308 T
1 T
5309 CGGTTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (19 bp):
TTGAGGCAGCTCATTTGTT
Found at i:9644 original size:13 final size:13
Alignment explanation
Indices: 9628--9658 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
9618 ATCTGATTAT
9628 ATTATCTATACTA
1 ATTATCTATACTA
9641 ATTATCTATACTA
1 ATTATCTATACTA
9654 ATTAT
1 ATTAT
9659 AATGTGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTATCTATACTA
Found at i:9659 original size:22 final size:22
Alignment explanation
Indices: 9644--9688 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
9634 TATACTAATT
*
9644 ATCTATACTAATTATAATGTGA
1 ATCTATACTAATTATAATATGA
*
9666 ATCTATACTAATTATAATGTGA
1 ATCTATACTAATTATAATATGA
9688 A
1 A
9689 ATCCTGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
ATCTATACTAATTATAATATGA
Found at i:9907 original size:133 final size:133
Alignment explanation
Indices: 9669--9938 Score: 504
Period size: 133 Copynumber: 2.0 Consensus size: 133
9659 AATGTGAATC
*
9669 TATACTAATTATAATGTGAAATCCTGAGTTTGTGTCACGAGTTGACTCGGATACAAACTCAGTTT
1 TATACTAATTATAATGTGAAATCCTGAGTTTGTGTCACGAGTTGACTCGAATACAAACTCAGTTT
* *
9734 TTAAAAGATTAAAAACTACCCATTTGAAAATAAATCACCAAGGATATATATAATAATTAATTTTT
66 TTAAAAGATTAAAAACTACCAATTTGAAAATAAACCACCAAGGATATATATAATAATTAATTTTT
9799 ATT
131 ATT
*
9802 TATACTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTGACTCGAATACAAACTCAGTTT
1 TATACTAATTATAATGTGAAATCCTGAGTTTGTGTCACGAGTTGACTCGAATACAAACTCAGTTT
9867 TTAAAAGATTAAAAACTACCAATTTGAAAATAAACCACCAAGGATATATATAATAATTAATTTTT
66 TTAAAAGATTAAAAACTACCAATTTGAAAATAAACCACCAAGGATATATATAATAATTAATTTTT
9932 ATT
131 ATT
9935 TATA
1 TATA
9939 TCATTTAAAA
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (133 bp):
TATACTAATTATAATGTGAAATCCTGAGTTTGTGTCACGAGTTGACTCGAATACAAACTCAGTTT
TTAAAAGATTAAAAACTACCAATTTGAAAATAAACCACCAAGGATATATATAATAATTAATTTTT
ATT
Found at i:10127 original size:15 final size:15
Alignment explanation
Indices: 10084--10124 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
10074 CATGATAATG
10084 ATAATTATAATTATA
1 ATAATTATAATTATA
10099 ATAATTATAATTAT-
1 ATAATTATAATTATA
*
10113 ATAATTAAAATT
1 ATAATTATAATT
10125 TATTGTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATTATAATTATA
Found at i:10421 original size:29 final size:29
Alignment explanation
Indices: 10388--10453 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
10378 TAAATAAATT
10388 AAATTG-AGCATGTCTAAAGGTTTAGGACC
1 AAATTGAAGCATGTC-AAAGGTTTAGGACC
* *
10417 AAATTGAATATCTTGTCAAAGGTTTAGGACC
1 AAATTG-A-AGCATGTCAAAGGTTTAGGACC
10448 AAATTG
1 AAATTG
10454 GGCTTTTAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 6 0.19
31 20 0.62
32 6 0.19
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (29 bp):
AAATTGAAGCATGTCAAAGGTTTAGGACC
Done.