Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001094.1 Corchorus capsularis cultivar CVL-1 contig01094, 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: 15267
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2021 original size:47 final size:47
Alignment explanation
Indices: 1952--2046 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1942 TACGTACCCT
1952 ACCCATCTCAATCTTCCTGTTGAAAATCTAAAAAAGTAGTATTTTTA
1 ACCCATCTCAATCTTCCTGTTGAAAATCTAAAAAAGTAGTATTTTTA
1999 ACCCATCTCAATCTTCCTGTTGAAAATCTAAAAAAGTAGTATTTTTA
1 ACCCATCTCAATCTTCCTGTTGAAAATCTAAAAAAGTAGTATTTTTA
2046 A
1 A
2047 TTACAGTCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (47 bp):
ACCCATCTCAATCTTCCTGTTGAAAATCTAAAAAAGTAGTATTTTTA
Found at i:4610 original size:16 final size:13
Alignment explanation
Indices: 4574--4631 Score: 89
Period size: 13 Copynumber: 4.2 Consensus size: 13
4564 TACCCGTCGG
4574 TATCCGGTAGTCT
1 TATCCGGTAGTCT
4587 TATCCGGTAGTCT
1 TATCCGGTAGTCT
4600 TATTGTCCGGTAGTCT
1 TA---TCCGGTAGTCT
4616 TATCCGGTAGTCT
1 TATCCGGTAGTCT
4629 TAT
1 TAT
4632 TGAACGTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
13 29 0.69
16 13 0.31
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (13 bp):
TATCCGGTAGTCT
Found at i:4618 original size:29 final size:29
Alignment explanation
Indices: 4576--4633 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
4566 CCCGTCGGTA
4576 TCCGGTAGTCTTATCCGGTAGTCTTATTG
1 TCCGGTAGTCTTATCCGGTAGTCTTATTG
4605 TCCGGTAGTCTTATCCGGTAGTCTTATTG
1 TCCGGTAGTCTTATCCGGTAGTCTTATTG
4634 AACGTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (29 bp):
TCCGGTAGTCTTATCCGGTAGTCTTATTG
Found at i:5010 original size:88 final size:88
Alignment explanation
Indices: 4861--5037 Score: 345
Period size: 88 Copynumber: 2.0 Consensus size: 88
4851 AAAGTGCAAA
4861 ATTGATGTAATTAATCTTAGGGTTTTGATTTTGCTTGACAATTTGGTGGCCGAAGTTGATGGCCA
1 ATTGATGTAATTAATCTTAGGGTTTTGATTTTGCTTGACAATTTGGTGGCCGAAGTTGATGGCCA
4926 AGTTTAATTAATCAAACGAGCAT
66 AGTTTAATTAATCAAACGAGCAT
*
4949 ATTGATGTAATTAATCTTAGGGTTTTGATTTTGCTTGACAATTTGGTGGCCGAAGTTGATGGCTA
1 ATTGATGTAATTAATCTTAGGGTTTTGATTTTGCTTGACAATTTGGTGGCCGAAGTTGATGGCCA
5014 AGTTTAATTAATCAAACGAGCAT
66 AGTTTAATTAATCAAACGAGCAT
5037 A
1 A
5038 GGAAGGCCAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.38
Consensus pattern (88 bp):
ATTGATGTAATTAATCTTAGGGTTTTGATTTTGCTTGACAATTTGGTGGCCGAAGTTGATGGCCA
AGTTTAATTAATCAAACGAGCAT
Found at i:9922 original size:31 final size:32
Alignment explanation
Indices: 9887--9957 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
9877 TAGTGGCTGT
* **
9887 GCCGCCCC-GGGGGGCGGTTTGCCGTGGCAAA
1 GCCGCCCCAGCGGGGCGGCCTGCCGTGGCAAA
* *
9918 GCCGCCCCAGCTGTGCGGCCTGCCGTGGCAAA
1 GCCGCCCCAGCGGGGCGGCCTGCCGTGGCAAA
*
9950 CCCGCCCC
1 GCCGCCCC
9958 CCTGCGGCGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.10, C:0.42, G:0.37, T:0.11
Consensus pattern (32 bp):
GCCGCCCCAGCGGGGCGGCCTGCCGTGGCAAA
Found at i:9968 original size:32 final size:32
Alignment explanation
Indices: 9906--9968 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
9896 GGGGGCGGTT
* * *
9906 TGCCGTGGCAAAGCCGCCCCAGCTGTGCGGCC
1 TGCCGTGGCAAACCCGCCCCACCTGGGCGGCC
9938 TGCCGTGGCAAACCCGCCCC-CCTGCGGCGGC
1 TGCCGTGGCAAACCCGCCCCACCTG-GGCGGC
9969 TAGGCCTCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.11, C:0.44, G:0.33, T:0.11
Consensus pattern (32 bp):
TGCCGTGGCAAACCCGCCCCACCTGGGCGGCC
Found at i:10517 original size:27 final size:27
Alignment explanation
Indices: 10487--10596 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 27
10477 TTGATGAGTT
*
10487 TGAGTGTGCTCAGCCGGGTTACTATGA
1 TGAGGGTGCTCAGCCGGGTTACTATGA
* *
10514 TGAGGGTGTTCAGTCGGGTTACTATGA
1 TGAGGGTGCTCAGCCGGGTTACTATGA
* * *
10541 TAAGGGTGCTCAGCCCGATTACTATGA
1 TGAGGGTGCTCAGCCGGGTTACTATGA
* *
10568 TG-GGGCAGCTCAGCCAGGTTACTATGA
1 TGAGGG-TGCTCAGCCGGGTTACTATGA
10595 TG
1 TG
10597 GGGCCGAGGA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
26 3 0.04
27 67 0.96
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (27 bp):
TGAGGGTGCTCAGCCGGGTTACTATGA
Done.