Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007871.1 Corchorus capsularis cultivar CVL-1 contig07892, 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: 5752
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Found at i:1744 original size:63 final size:63
Alignment explanation
Indices: 1667--1806 Score: 176
Period size: 63 Copynumber: 2.2 Consensus size: 63
1657 TCAGGTTGGG
* * * * *
1667 TTCGGGCTCGGGTT-A-TCGGGTTCGGGCTTGAGTCGGGTTCGGGTTGGATTTGGGTCAGTTTAA
1 TTCGGGTTCGGGTTAATTCGGG-TCAGG-TTAAGTCGGGTTCAGGTTGAATTTGGGTCAGTTTAA
* * *
1730 TTCGGGTTCGGGTTAATTTGGGTCAGGTTAATTTGGGTTCAGGTTGAATTTGGGTCAGTTTAA
1 TTCGGGTTCGGGTTAATTCGGGTCAGGTTAAGTCGGGTTCAGGTTGAATTTGGGTCAGTTTAA
1793 TTCGGGTTCGGGTT
1 TTCGGGTTCGGGTT
1807 CTGTTTGGGT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 58 0.87
64 5 0.07
65 4 0.06
ACGTcount: A:0.12, C:0.11, G:0.38, T:0.39
Consensus pattern (63 bp):
TTCGGGTTCGGGTTAATTCGGGTCAGGTTAAGTCGGGTTCAGGTTGAATTTGGGTCAGTTTAA
Found at i:1752 original size:31 final size:32
Alignment explanation
Indices: 1699--1806 Score: 173
Period size: 32 Copynumber: 3.4 Consensus size: 32
1689 CGGGCTTGAG
*
1699 TCGGGTTCGGGTTGGATTTGGGTCAGTTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGTTTAAT
*
1731 TCGGGTTCGGGTT-AATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGTTTAAT
* *
1762 TTGGGTTCAGGTTGAATTTGGGTCAGTTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGTTTAAT
1794 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
1807 CTGTTTGGGT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 27 0.40
32 41 0.60
ACGTcount: A:0.14, C:0.09, G:0.36, T:0.41
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGTTTAAT
Found at i:1760 original size:15 final size:15
Alignment explanation
Indices: 1714--1799 Score: 100
Period size: 15 Copynumber: 5.5 Consensus size: 15
1704 TTCGGGTTGG
*
1714 ATTTGGGTCAGTTTA
1 ATTTGGGTCAGGTTA
* *
1729 ATTCGGGTTCGGGTTA
1 ATTTGGG-TCAGGTTA
1745 ATTTGGGTCAGGTTA
1 ATTTGGGTCAGGTTA
1760 ATTTGGGTTCAGGTTGA
1 ATTTGGG-TCAGGTT-A
*
1777 ATTTGGGTCAGTTTA
1 ATTTGGGTCAGGTTA
*
1792 ATTCGGGT
1 ATTTGGGT
1800 TCGGGTTCTG
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
15 28 0.46
16 25 0.41
17 8 0.13
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (15 bp):
ATTTGGGTCAGGTTA
Found at i:1975 original size:16 final size:16
Alignment explanation
Indices: 1954--2043 Score: 108
Period size: 16 Copynumber: 5.6 Consensus size: 16
1944 TTTTCATAAA
* *
1954 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGAGTT
*
1970 TTTTCGGGTTTGAGTT
1 TTTTCGGGTTCGAGTT
*
1986 TTTTCGGGTTCGGGTT
1 TTTTCGGGTTCGAGTT
* *
2002 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGAGTT
* *
2018 ATTTCGGGTTCGTGTT
1 TTTTCGGGTTCGAGTT
2034 TTTTCGGGTT
1 TTTTCGGGTT
2044 TGAACTTTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 61 1.00
ACGTcount: A:0.04, C:0.11, G:0.32, T:0.52
Consensus pattern (16 bp):
TTTTCGGGTTCGAGTT
Found at i:1998 original size:32 final size:32
Alignment explanation
Indices: 1954--2065 Score: 154
Period size: 32 Copynumber: 3.5 Consensus size: 32
1944 TTTTCATAAA
*
1954 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGTT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGTT
*
1986 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGTT
* * *
2018 ATTTCGGGTTCGTGTTTTTTCGGGTTTGAACTT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTG-AGTT
*
2051 TTTT-GGGTTCAGGTT
1 TTTTCGGGTTCGGGTT
2066 CAGGCGGGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
32 65 0.93
33 5 0.07
ACGTcount: A:0.06, C:0.11, G:0.31, T:0.52
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGTT
Found at i:2052 original size:16 final size:16
Alignment explanation
Indices: 1967--2059 Score: 107
Period size: 16 Copynumber: 5.8 Consensus size: 16
1957 TCGGATTCGG
1967 GTTTTTTCGGGTTTGA
1 GTTTTTTCGGGTTTGA
* *
1983 GTTTTTTCGGGTTCGG
1 GTTTTTTCGGGTTTGA
1999 GTTTTTTCGGGTTTGA
1 GTTTTTTCGGGTTTGA
* * * *
2015 GCTATTTCGGGTTCGT
1 GTTTTTTCGGGTTTGA
2031 GTTTTTTCGGGTTTGAA
1 GTTTTTTCGGGTTTG-A
*
2048 CTTTTTT-GGGTT
1 GTTTTTTCGGGTT
2060 CAGGTTCAGG
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
16 57 0.90
17 6 0.10
ACGTcount: A:0.05, C:0.10, G:0.31, T:0.54
Consensus pattern (16 bp):
GTTTTTTCGGGTTTGA
Found at i:2149 original size:15 final size:16
Alignment explanation
Indices: 2129--2158 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2119 CGGGATCAAG
2129 TTTTCGGG-CGGGTTT
1 TTTTCGGGTCGGGTTT
2144 TTTTCGGGTCGGGTT
1 TTTTCGGGTCGGGTT
2159 CACTTTGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.13, G:0.40, T:0.47
Consensus pattern (16 bp):
TTTTCGGGTCGGGTTT
Done.