Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010780.1 Corchorus capsularis cultivar CVL-1 contig10801, 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: 14022
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Found at i:1441 original size:22 final size:23
Alignment explanation
Indices: 1393--1447 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
1383 CAATGAAATT
*
1393 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACACTATGAGATA
** *
1416 TTGATAACCTTCA-TATGATATA
1 TTGATAACCAACACTATGAGATA
1438 TTGATAACCA
1 TTGATAACCA
1448 CGTTATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (23 bp):
TTGATAACCAACACTATGAGATA
Found at i:1511 original size:22 final size:22
Alignment explanation
Indices: 1486--1554 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
1476 GAATTGTTAG
*
1486 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
1508 TAATCGCATTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
1530 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
1552 TAA
1 TAA
1555 AATTTTGATA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:1583 original size:23 final size:23
Alignment explanation
Indices: 1551--1611 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1541 TGAAATTTTG
* * *
1551 ATAAAATTTTGATATATCTTCCT
1 ATAAAATTTTGATAAATCTCCCC
*
1574 ATAAAGTTTTGATAAATCTCCCC
1 ATAAAATTTTGATAAATCTCCCC
1597 ATAAAATTTTGATAA
1 ATAAAATTTTGATAA
1612 CTTTCTTATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (23 bp):
ATAAAATTTTGATAAATCTCCCC
Found at i:2097 original size:22 final size:22
Alignment explanation
Indices: 2046--2171 Score: 105
Period size: 22 Copynumber: 5.7 Consensus size: 22
2036 ATAACATTCA
* *
2046 TATGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCTCAC
* *
2068 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
2090 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCTCAC
* *
2111 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCTCAC
*
2134 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCAC
* *
2156 GATGACATTTTGATAA
1 TATGAAATTTTGATAA
2172 TCTCTTTGAT
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
21 4 0.05
22 74 0.90
23 4 0.05
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:4079 original size:30 final size:31
Alignment explanation
Indices: 4043--4107 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
4033 CCTAAAAAAA
* * *
4043 GAAATATATTTTTAAAA-AATGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
*
4073 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
4104 GAAA
1 GAAA
4108 AGATAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:8324 original size:22 final size:22
Alignment explanation
Indices: 8296--8340 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
8286 ACTAACTAGA
8296 GCTACTTCAATATTGGGAGTGT
1 GCTACTTCAATATTGGGAGTGT
8318 GCTACTTCAATATTGGGAGTGT
1 GCTACTTCAATATTGGGAGTGT
8340 G
1 G
8341 AAAACAGTAG
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:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (22 bp):
GCTACTTCAATATTGGGAGTGT
Found at i:8429 original size:30 final size:30
Alignment explanation
Indices: 8395--8455 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
8385 ATATGTGTGA
8395 TTTTTTTGGTGCAGAGAGAAAGACTAATAC
1 TTTTTTTGGTGCAGAGAGAAAGACTAATAC
8425 TTTTTTTGGTGCAGAGAGAAAGACTAATAC
1 TTTTTTTGGTGCAGAGAGAAAGACTAATAC
8455 T
1 T
8456 CCACCAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (30 bp):
TTTTTTTGGTGCAGAGAGAAAGACTAATAC
Found at i:8631 original size:47 final size:47
Alignment explanation
Indices: 8580--8674 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
8570 TTTACTAGTC
* *
8580 ACCACCGCTCTTTTGGACTATTTTACCCTTTTCTTTATTTTCCTTCA
1 ACCACCGCCCTCTTGGACTATTTTACCCTTTTCTTTATTTTCCTTCA
*
8627 ACCACCGCCCTCTTGGACTATTTTACCTTTTTCTTTATTTTCCTTCA
1 ACCACCGCCCTCTTGGACTATTTTACCCTTTTCTTTATTTTCCTTCA
8674 A
1 A
8675 ACTTTAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.16, C:0.31, G:0.06, T:0.47
Consensus pattern (47 bp):
ACCACCGCCCTCTTGGACTATTTTACCCTTTTCTTTATTTTCCTTCA
Done.