Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008858.1 Corchorus capsularis cultivar CVL-1 contig08879, 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: 16089
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4658 original size:2 final size:2
Alignment explanation
Indices: 4653--4758 Score: 61
Period size: 2 Copynumber: 58.0 Consensus size: 2
4643 TTACACACAC
*
4653 AT AT AT AT AT AT AT AT -T AC AT AT -T A- AT A- AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
4690 AT AT AT -T A- AA AT A- AA AT TT TT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
4729 AT -T CT -T AT TT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4759 TCTTATTTAA
Statistics
Matches: 82, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
1 10 0.12
2 72 0.88
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4677 original size:7 final size:7
Alignment explanation
Indices: 4654--4697 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
4644 TACACACACA
4654 TATATAT
1 TATATAT
4661 ATATATAT
1 -TATATAT
*
4669 TACATAT
1 TATATAT
*
4676 TA-ATAA
1 TATATAT
4682 TATATAT
1 TATATAT
4689 TATATAT
1 TATATAT
4696 TA
1 TA
4698 AAATAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
6 5 0.16
7 20 0.62
8 7 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (7 bp):
TATATAT
Found at i:4739 original size:28 final size:28
Alignment explanation
Indices: 4708--4767 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
4698 AAATAAAATT
4708 TTTACATATATATATATATATATTCTTA
1 TTTACATATATATATATATATATTCTTA
4736 TTTACATATATATATATATATATTCTTA
1 TTTACATATATATATATATATATTCTTA
4764 TTTA
1 TTTA
4768 ATAAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTACATATATATATATATATATTCTTA
Found at i:4776 original size:28 final size:28
Alignment explanation
Indices: 4708--4776 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
4698 AAATAAAATT
*
4708 TTTACATATATATATATATATATTCTTA
1 TTTACATAAATATATATATATATTCTTA
*
4736 TTTACATATATATATATATATATTCTTA
1 TTTACATAAATATATATATATATTCTTA
4764 TTTA-ATAAA-ATAT
1 TTTACATAAATATAT
4777 TTTACATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 4 0.10
27 4 0.10
28 32 0.80
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTACATAAATATATATATATATTCTTA
Found at i:4811 original size:90 final size:89
Alignment explanation
Indices: 4653--4821 Score: 216
Period size: 90 Copynumber: 1.9 Consensus size: 89
4643 TTACACACAC
* * * *
4653 ATATATATATATATATTACATATTAATAATATATATTATATATTAAAATAAAATTTTTACATATA
1 ATATATATATATATATTACATATTAATAAAATATATTACATATTAAAATAAAATTTTTATAGATA
4718 TATATATATATATTCTTATTTACAT
66 TATATA-ATATATTCTTATTTACAT
* * *
4743 ATATATATATATATATT-CTTATTTAATAAAATATTTTACATATTAAAATAAAAATGATTTT-TG
1 ATATATATATATATATTACATA-TTAATAAAATATATTACATATTAAAAT-AAAAT--TTTTATA
4806 GATATATATAATATAT
62 GATATATATAATATAT
4822 ATAATTAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
89 3 0.04
90 41 0.60
91 11 0.16
92 9 0.13
93 4 0.06
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.48
Consensus pattern (89 bp):
ATATATATATATATATTACATATTAATAAAATATATTACATATTAAAATAAAATTTTTATAGATA
TATATAATATATTCTTATTTACAT
Found at i:4988 original size:18 final size:18
Alignment explanation
Indices: 4965--4999 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4955 CCGACTTCAC
*
4965 AAACCGAATCACCCGACA
1 AAACCGAATCAACCGACA
*
4983 AAACCGATTCAACCGAC
1 AAACCGAATCAACCGAC
5000 CCATTTCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.37, G:0.11, T:0.09
Consensus pattern (18 bp):
AAACCGAATCAACCGACA
Found at i:6667 original size:24 final size:24
Alignment explanation
Indices: 6606--6670 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 24
6596 TAATTTGAAT
*
6606 GAATTGAGAACCAGACCAAGGGCA
1 GAATTGAGAACCAGACCAAGGGAA
**
6630 GAA-TGA-ATTC---CCAAGGGAA
1 GAATTGAGAACCAGACCAAGGGAA
6649 GAATTGAGAACCAGACCAAGGG
1 GAATTGAGAACCAGACCAAGGG
6671 CATGACGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
19 11 0.35
20 3 0.10
21 2 0.06
22 2 0.06
23 3 0.10
24 10 0.32
ACGTcount: A:0.42, C:0.18, G:0.29, T:0.11
Consensus pattern (24 bp):
GAATTGAGAACCAGACCAAGGGAA
Found at i:9658 original size:13 final size:13
Alignment explanation
Indices: 9621--9649 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9611 GTTAAGTAAT
9621 AGTTAGTTATATG
1 AGTTAGTTATATG
9634 AGTTAGTTATATG
1 AGTTAGTTATATG
9647 AGT
1 AGT
9650 CTTGTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (13 bp):
AGTTAGTTATATG
Found at i:14549 original size:13 final size:13
Alignment explanation
Indices: 14531--14555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14521 GTTAAGTAAT
14531 AGTTAGTTATATG
1 AGTTAGTTATATG
14544 AGTTAGTTATAT
1 AGTTAGTTATAT
14556 TAGTCTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AGTTAGTTATATG
Done.