Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005507.1 Corchorus capsularis cultivar CVL-1 contig05525, 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: 4098
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Found at i:1735 original size:40 final size:42
Alignment explanation
Indices: 1660--1759 Score: 136
Period size: 40 Copynumber: 2.5 Consensus size: 42
1650 GGAAAGAGAT
*
1660 TAATCAGTGAAATCAGTAATTAAAGAGTCAAAGTAAAAGAAG
1 TAATCAGTAAAATCAGTAATTAAAGAGTCAAAGTAAAAGAAG
* *
1702 TAATCAGTAAAAT-GGTAATT-AAGAGT-AGGAGTAAAAGAAG
1 TAATCAGTAAAATCAGTAATTAAAGAGTCA-AAGTAAAAGAAG
1742 TAATCAGT-AAATCAGTAA
1 TAATCAGTAAAATCAGTAA
1760 AGAGCAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
39 5 0.10
40 29 0.56
41 6 0.12
42 12 0.23
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (42 bp):
TAATCAGTAAAATCAGTAATTAAAGAGTCAAAGTAAAAGAAG
Found at i:1910 original size:44 final size:43
Alignment explanation
Indices: 1788--2023 Score: 244
Period size: 42 Copynumber: 5.7 Consensus size: 43
1778 AGTAAAGGGG
* *
1788 AATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAA-GGT
1 AATCAGTAAAAGCAAAATGGTAATCAGTAAAGAGTAAAATAGT
*
1830 AATCAGTAAGAGCAAAATGGTAATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAAGCAAAATGGTAATCAGTAAAGAGTAAAATAGT
*
1873 AATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAATAG-
1 AATCAGT-AAAAGCAA-AATGGTAATCAGTAAAGAGTAAAATAGT
* * *
1916 --T-A--AAAAG--TAATGATAATCAGTAAAGGGTAAAATAGT
1 AATCAGTAAAAGCAAAATGGTAATCAGTAAAGAGTAAAATAGT
* * * *
1952 AATCAGTAAGAGCAAAGTGGTTATTAGT-AAGAGTAAAATAGT
1 AATCAGTAAAAGCAAAATGGTAATCAGTAAAGAGTAAAATAGT
* *
1994 AATCTGTAAAGAGTAAAA-GGTAATCAGTAA
1 AATCAGTAAA-AGCAAAATGGTAATCAGTAA
2024 TTCAGAGAGT
Statistics
Matches: 161, Mismatches: 19, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
34 2 0.01
35 22 0.14
37 5 0.03
38 1 0.01
39 1 0.01
40 1 0.01
41 5 0.03
42 68 0.42
43 24 0.15
44 30 0.19
45 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.22, T:0.22
Consensus pattern (43 bp):
AATCAGTAAAAGCAAAATGGTAATCAGTAAAGAGTAAAATAGT
Found at i:1917 original size:15 final size:15
Alignment explanation
Indices: 1855--1953 Score: 62
Period size: 15 Copynumber: 6.3 Consensus size: 15
1845 AATGGTAATC
1855 AGTAAAGAGTAAAAT
1 AGTAAAGAGTAAAAT
**
1870 AGTAATCAGTAAAA-
1 AGTAAAGAGTAAAAT
1884 AGT-AAGAAGGT--AAT
1 AGTAAAG-A-GTAAAAT
1898 CAGTAAAGAGTAAAAT
1 -AGTAAAGAGTAAAAT
*
1914 AGTAAAAAGTAATGATAAT
1 AGTAAAGAGT-A--A-AAT
*
1933 CAGTAAAGGGTAAAAT
1 -AGTAAAGAGTAAAAT
1949 AGTAA
1 AGTAA
1954 TCAGTAAGAG
Statistics
Matches: 65, Mismatches: 7, Indels: 24
0.68 0.07 0.25
Matches are distributed among these distances:
13 3 0.05
14 6 0.09
15 32 0.49
16 10 0.15
17 1 0.02
18 1 0.02
19 4 0.06
20 8 0.12
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.21
Consensus pattern (15 bp):
AGTAAAGAGTAAAAT
Found at i:1919 original size:8 final size:7
Alignment explanation
Indices: 1855--1925 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
1845 AATGGTAATC
*
1855 AGTAAAG
1 AGTAAAA
1862 AGTAAAA
1 AGTAAAA
**
1869 TAGTAATC
1 -AGTAAAA
1877 AGTAAAA
1 AGTAAAA
1884 AGTAAGAA
1 AGTAA-AA
* **
1892 GGTAATC
1 AGTAAAA
*
1899 AGTAAAG
1 AGTAAAA
1906 AGTAAAA
1 AGTAAAA
1913 TAGTAAAA
1 -AGTAAAA
1921 AGTAA
1 AGTAA
1926 TGATAATCAG
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
7 31 0.63
8 18 0.37
ACGTcount: A:0.58, C:0.03, G:0.20, T:0.20
Consensus pattern (7 bp):
AGTAAAA
Found at i:1925 original size:22 final size:22
Alignment explanation
Indices: 1788--1918 Score: 180
Period size: 22 Copynumber: 6.1 Consensus size: 22
1778 AGTAAAGGGG
*
1788 AATCAGT-AAGAGCAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
1809 AATCAGTAAAGAGTAAAA-GGT
1 AATCAGTAAAGAGTAAAATGGT
*
1830 AATCAGT-AAGAGCAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
*
1851 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
*
1873 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
*
1895 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
1917 AA
1 AA
1919 AAAGTAATGA
Statistics
Matches: 97, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
20 9 0.09
21 29 0.30
22 57 0.59
23 2 0.02
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.20
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGGT
Found at i:1940 original size:35 final size:36
Alignment explanation
Indices: 1877--1962 Score: 113
Period size: 35 Copynumber: 2.4 Consensus size: 36
1867 AATAGTAATC
1877 AGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAAT
1 AGTAAAAAGTAAGAA-GTAATCAGTAAAGAGTAAAAT
*
1914 AGTAAAAAGTAATG-A-TAATCAGTAAAGGGTAAAAT
1 AGTAAAAAGTAA-GAAGTAATCAGTAAAGAGTAAAAT
**
1949 AGTAATCAGTAAGA
1 AGTAAAAAGTAAGA
1963 GCAAAGTGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 1 0.02
35 29 0.66
37 13 0.30
38 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (36 bp):
AGTAAAAAGTAAGAAGTAATCAGTAAAGAGTAAAAT
Found at i:2016 original size:21 final size:22
Alignment explanation
Indices: 1929--2023 Score: 97
Period size: 21 Copynumber: 4.5 Consensus size: 22
1919 AAAGTAATGA
*
1929 TAATCAGTAAAGGGTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
* * *
1951 TAATCAGT-AAGAGCAAAGTGG
1 TAATCAGTAAAGAGTAAAATAG
* *
1972 TTATTAGT-AAGAGTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
* *
1993 TAATCTGTAAAGAGTAAAA-GG
1 TAATCAGTAAAGAGTAAAATAG
2014 TAATCAGTAA
1 TAATCAGTAA
2024 TTCAGAGAGT
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
21 40 0.69
22 18 0.31
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.25
Consensus pattern (22 bp):
TAATCAGTAAAGAGTAAAATAG
Found at i:2120 original size:27 final size:28
Alignment explanation
Indices: 2069--2134 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
2059 AAGAAGGGTA
2069 AAAAGTGGTAATCAATAAAAGAGAGTAAG
1 AAAAG-GGTAATCAATAAAAGAGAGTAAG
* * *
2098 GAAAGGGTAATTAGTAAAA-AGAGTAAG
1 AAAAGGGTAATCAATAAAAGAGAGTAAG
*
2125 AAAAGAGTAA
1 AAAAGGGTAA
2135 AAATGATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 16 0.50
28 12 0.38
29 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.17
Consensus pattern (28 bp):
AAAAGGGTAATCAATAAAAGAGAGTAAG
Done.