Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005885.1 Corchorus capsularis cultivar CVL-1 contig05903, 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: 2145
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Found at i:1625 original size:33 final size:34
Alignment explanation
Indices: 1578--1719 Score: 209
Period size: 33 Copynumber: 4.3 Consensus size: 34
1568 TTAGGCAAAA
1578 GAAAGAAGACTGAAATTAA-ACTGAAATTAGACT
1 GAAAGAAGACTGAAATTAAGACTGAAATTAGACT
*
1611 GAAAGAAGATTGAAATT-AGACTGAAATTAGACT
1 GAAAGAAGACTGAAATTAAGACTGAAATTAGACT
**
1644 GAAAGAAGACTGAAAAGAAGACTGAAATTAGACT
1 GAAAGAAGACTGAAATTAAGACTGAAATTAGACT
* **
1678 GAAAGAAGACTGAAA-TAAGACTGAGAGAAGACT
1 GAAAGAAGACTGAAATTAAGACTGAAATTAGACT
1711 GAAAGAAGA
1 GAAAGAAGA
1720 TTGGCTTAGT
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 67 0.68
34 31 0.31
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.17
Consensus pattern (34 bp):
GAAAGAAGACTGAAATTAAGACTGAAATTAGACT
Found at i:1687 original size:11 final size:11
Alignment explanation
Indices: 1578--1719 Score: 151
Period size: 11 Copynumber: 12.8 Consensus size: 11
1568 TTAGGCAAAA
1578 GAAAGAAGACT
1 GAAAGAAGACT
*
1589 GAAATTAA-ACT
1 GAAA-GAAGACT
**
1600 GAAATTAGACT
1 GAAAGAAGACT
*
1611 GAAAGAAGATT
1 GAAAGAAGACT
**
1622 GAAATTAGACT
1 GAAAGAAGACT
**
1633 GAAATTAGACT
1 GAAAGAAGACT
1644 GAAAGAAGACT
1 GAAAGAAGACT
1655 GAAAAGAAGACT
1 G-AAAGAAGACT
**
1667 GAAATTAGACT
1 GAAAGAAGACT
1678 GAAAGAAGACT
1 GAAAGAAGACT
*
1689 GAAATAAGACT
1 GAAAGAAGACT
*
1700 GAGAGAAGACT
1 GAAAGAAGACT
1711 GAAAGAAGA
1 GAAAGAAGA
1720 TTGGCTTAGT
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
10 2 0.02
11 95 0.86
12 13 0.12
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.17
Consensus pattern (11 bp):
GAAAGAAGACT
Found at i:1762 original size:36 final size:36
Alignment explanation
Indices: 1721--2145 Score: 557
Period size: 36 Copynumber: 11.8 Consensus size: 36
1711 GAAAGAAGAT
* * *
1721 TGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGAC
1 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
* *
1757 TGGCTTAATTTCAAGGAAATTAAGTAAAGAAAAGAT
1 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
* * *
1793 TGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGAC
1 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
*** * *
1829 TGGCTTAATTTCCTTGAAATTAAGTAAAGAAAAGAT
1 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
* * * *
1865 TGGCTTAGTTTCAAGGAAACTAGGTAATGAATAGAC
1 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
*
1901 TTGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
1 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
* * *
1937 TAGCTTAATTTCAAGGAAATTAGGTAAAGGAA-AGAT
1 TGGCTTAATTTCAAGGAAATTAAGTAAA-GAATAGAC
* *
1973 TGGCTTAATTTCAAGGAAATTAAGTAAAGAAAAGAT
1 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
* * *
2009 TGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGAC
1 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
2045 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
1 TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
* *
2081 TGGCTTAATTTCAAGGAAATTAGGTAAAGGAA-AGAT
1 TGGCTTAATTTCAAGGAAATTAAGTAAA-GAATAGAC
*
2117 TGGCTTAATTTTAAGGAAATTAAGTAAAG
1 TGGCTTAATTTCAAGGAAATTAAGTAAAG
Statistics
Matches: 337, Mismatches: 49, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
35 4 0.01
36 327 0.97
37 6 0.02
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (36 bp):
TGGCTTAATTTCAAGGAAATTAAGTAAAGAATAGAC
Found at i:1794 original size:72 final size:72
Alignment explanation
Indices: 1716--2145 Score: 675
Period size: 72 Copynumber: 6.0 Consensus size: 72
1706 AGACTGAAAG
1716 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
1 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
1781 TAAAGAA
66 TAAAGAA
***
1788 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCCTTGAAATTAAG
1 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
1853 TAAAGAA
66 TAAAGAA
* *
1860 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAATGAATAGACTTGCTTAATTTCAAGGAAATTAAG
1 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
1925 TAAAGAA
66 TAAAGAA
* * * * * *
1932 TAGACTAGCTTAATTTCAAGGAAATTAGGTAAAGGAA-AGATTGGCTTAATTTCAAGGAAATTAA
1 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAA-GAATAGACTGGCTTAATTTCAAGGAAATTAA
1996 GTAAAGAA
65 GTAAAGAA
2004 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
1 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
2069 TAAAGAA
66 TAAAGAA
* * * * * *
2076 TAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGAA-AGATTGGCTTAATTTTAAGGAAATTAA
1 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAA-GAATAGACTGGCTTAATTTCAAGGAAATTAA
2140 GTAAAG
65 GTAAAG
Statistics
Matches: 327, Mismatches: 28, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
71 3 0.01
72 318 0.97
73 6 0.02
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (72 bp):
AAGATTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAG
TAAAGAA
Done.