Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009339.1 Corchorus capsularis cultivar CVL-1 contig09360, 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: 15710
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:1906 original size:18 final size:18
Alignment explanation
Indices: 1843--1961 Score: 58
Period size: 18 Copynumber: 6.9 Consensus size: 18
1833 GGGAAGGAGG
*
1843 AGTGTGTGAAGGTGTGAT
1 AGTGGGTGAAGGTGTGAT
* *
1861 GGTTGGTG-AGG-GATG-T
1 AGTGGGTGAAGGTG-TGAT
* *
1877 -GTGGATGGAGGTGTGAT
1 AGTGGGTGAAGGTGTGAT
1894 AGTGGGTGAAGGTGTGAT
1 AGTGGGTGAAGGTGTGAT
* *
1912 GGTTGGTG-AGG-GATG-T
1 AGTGGGTGAAGGTG-TGAT
*
1928 -GTGGATGGAA-GTGTGAT
1 AGTGGGT-GAAGGTGTGAT
*
1945 AGTGGGTAAAGGATGTG
1 AGTGGGTGAAGG-TGTG
1962 TGGGGGAAGG
Statistics
Matches: 75, Mismatches: 13, Indels: 25
0.66 0.12 0.22
Matches are distributed among these distances:
15 9 0.12
16 13 0.17
17 17 0.23
18 32 0.43
19 4 0.05
ACGTcount: A:0.20, C:0.00, G:0.50, T:0.29
Consensus pattern (18 bp):
AGTGGGTGAAGGTGTGAT
Found at i:1916 original size:51 final size:51
Alignment explanation
Indices: 1843--2046 Score: 212
Period size: 51 Copynumber: 4.2 Consensus size: 51
1833 GGGAAGGAGG
* *
1843 AGTGTGTGAAGGTGTGATGGTTGGTGAGGGATGTGTGGATGGAGGTGTGAT
1 AGTGGGTGAAGGTGTGATGGTTGGTGAGGGATGTGTGGATGGAAGTGTGAT
1894 AGTGGGTGAAGGTGTGATGGTTGGTGAGGGATGTGTGGATGGAAGTGTGAT
1 AGTGGGTGAAGGTGTGATGGTTGGTGAGGGATGTGTGGATGGAAGTGTGAT
* * ** *
1945 AGTGGGTAAAGGATGTG-TGG--GG-GAAGGA-G-AAGG--GGAAG-GAGA-
1 AGTGGGTGAAGG-TGTGATGGTTGGTGAGGGATGTGTGGATGGAAGTGTGAT
* * * * *
1987 AGTGGATGAAGGTGTGATGGTTTGTAAGGGATGTGTGGATGGATGTGCGAT
1 AGTGGGTGAAGGTGTGATGGTTGGTGAGGGATGTGTGGATGGAAGTGTGAT
*
2038 GGTGGGTGA
1 AGTGGGTGA
2047 CGGATGTGTA
Statistics
Matches: 124, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
41 4 0.03
42 13 0.10
43 3 0.02
44 6 0.05
45 4 0.03
46 3 0.02
47 3 0.02
48 5 0.04
49 6 0.05
50 3 0.02
51 70 0.56
52 4 0.03
ACGTcount: A:0.22, C:0.00, G:0.51, T:0.26
Consensus pattern (51 bp):
AGTGGGTGAAGGTGTGATGGTTGGTGAGGGATGTGTGGATGGAAGTGTGAT
Found at i:1959 original size:33 final size:33
Alignment explanation
Indices: 1922--2063 Score: 86
Period size: 33 Copynumber: 4.5 Consensus size: 33
1912 GGTTGGTGAG
1922 GGATGTGTGGATGGAAGTGTGATAGTGGGTAAA
1 GGATGTGTGGATGGAAGTGTGATAGTGGGTAAA
* *
1955 GGATGTGTGG-GGGAAG-GAGA-AG-GGG--AA
1 GGATGTGTGGATGGAAGTGTGATAGTGGGTAAA
* * ** *
1982 GGA-GAAGTGGAT-GAAGGTGTGATGGTTTGTAAG
1 GGATG-TGTGGATGGAA-GTGTGATAGTGGGTAAA
* * * * *
2015 GGATGTGTGGATGGATGTGCGATGGTGGGTGAC
1 GGATGTGTGGATGGAAGTGTGATAGTGGGTAAA
*
2048 GGATGTGTAGA-GGAAG
1 GGATGTGTGGATGGAAG
2064 GATTCAAGTA
Statistics
Matches: 81, Mismatches: 18, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
26 1 0.01
27 12 0.15
28 1 0.01
29 6 0.07
30 3 0.04
31 4 0.05
32 9 0.11
33 42 0.52
34 3 0.04
ACGTcount: A:0.25, C:0.01, G:0.50, T:0.23
Consensus pattern (33 bp):
GGATGTGTGGATGGAAGTGTGATAGTGGGTAAA
Found at i:1981 original size:12 final size:12
Alignment explanation
Indices: 1964--1988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1954 AGGATGTGTG
1964 GGGGAAGGAGAA
1 GGGGAAGGAGAA
1976 GGGGAAGGAGAA
1 GGGGAAGGAGAA
1988 G
1 G
1989 TGGATGAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (12 bp):
GGGGAAGGAGAA
Found at i:2006 original size:93 final size:93
Alignment explanation
Indices: 1894--2065 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
1884 GAGGTGTGAT
* * *
1894 AGTGGGTGAAGGTGTGATGGTTGGTGAGGGATGTGTGGATGGAAGTGTGATAGTGGGTAAAGGAT
1 AGTGGATGAAGGTGTGATGGTTGGTAAGGGATGTGTGGATGGAAGTGCGATAGTGGGTAAAGGAT
* *
1959 GTGTGGGGGAAGGAGAAGGGGAAGGAGA
66 GTGTAGAGGAAGGAGAAGGGGAAGGAGA
* * * * *
1987 AGTGGATGAAGGTGTGATGGTTTGTAAGGGATGTGTGGATGGATGTGCGATGGTGGGTGACGGAT
1 AGTGGATGAAGGTGTGATGGTTGGTAAGGGATGTGTGGATGGAAGTGCGATAGTGGGTAAAGGAT
2052 GTGTAGAGGAAGGA
66 GTGTAGAGGAAGGA
2066 TTCAAGTACC
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.24, C:0.01, G:0.51, T:0.24
Consensus pattern (93 bp):
AGTGGATGAAGGTGTGATGGTTGGTAAGGGATGTGTGGATGGAAGTGCGATAGTGGGTAAAGGAT
GTGTAGAGGAAGGAGAAGGGGAAGGAGA
Found at i:6968 original size:14 final size:15
Alignment explanation
Indices: 6949--6981 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
6939 AATGGCCAAG
6949 TTTTGTAACAGAAT-
1 TTTTGTAACAGAATA
6963 TTTTGTAACAGAATA
1 TTTTGTAACAGAATA
6978 TTTT
1 TTTT
6982 CCCGATACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (15 bp):
TTTTGTAACAGAATA
Found at i:8161 original size:104 final size:104
Alignment explanation
Indices: 7981--8173 Score: 332
Period size: 104 Copynumber: 1.9 Consensus size: 104
7971 CTGTCAGAAA
*
7981 AGTATTAGTCGATGAAAACTTCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
1 AGTATTAGTCGATGAAAACTCCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
*
8046 CTTTGAAAAAGTGGCAGTGTTGACAGCGAACCTGGAGGC
66 CTTTGAAAAAGTAGCAGTGTTGACAGCGAACCTGGAGGC
* * * *
8085 AGTATTAGTTGATGAAAACTCCAGTTTTAATTTCAGTATTAATCGACTAAAGCTCCAAGTCTTCA
1 AGTATTAGTCGATGAAAACTCCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
8150 CTTTGAAAAAGTAGCAGTGTTGAC
66 CTTTGAAAAAGTAGCAGTGTTGAC
8174 GACCACACGA
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 83 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (104 bp):
AGTATTAGTCGATGAAAACTCCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
CTTTGAAAAAGTAGCAGTGTTGACAGCGAACCTGGAGGC
Found at i:13105 original size:9 final size:9
Alignment explanation
Indices: 13080--13108 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
13070 CTCTCCACGT
13080 CCCCCCCC-
1 CCCCCCCCA
13088 CCCCCCCCA
1 CCCCCCCCA
13097 CCCCCCCCA
1 CCCCCCCCA
13106 CCC
1 CCC
13109 ACACACACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.07, C:0.93, G:0.00, T:0.00
Consensus pattern (9 bp):
CCCCCCCCA
Found at i:13124 original size:2 final size:2
Alignment explanation
Indices: 13119--13146 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13109 ACACACACAC
13119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13147 GCATGATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13418 original size:30 final size:31
Alignment explanation
Indices: 13345--13419 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
13335 ACACCTGTTT
* * *
13345 TTTATACTCAAATTGATCAACTTTTGAAAGG
1 TTTAGACTCAAATTAAGCAACTTTTGAAAGG
*
13376 TTTAGCCTCAAATTAAGCAACTTTTGAAAGG
1 TTTAGACTCAAATTAAGCAACTTTTGAAAGG
13407 -TTAGACTCAAATT
1 TTTAGACTCAAATT
13420 GGTGGCTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 12 0.31
31 27 0.69
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (31 bp):
TTTAGACTCAAATTAAGCAACTTTTGAAAGG
Found at i:13781 original size:22 final size:22
Alignment explanation
Indices: 13734--13782 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
13724 TGAATATTTT
* * *
13734 TATGAAATTTTGATAATTTACC
1 TATGAAATTGTGATAACTTACA
13756 TATGAAATTGTGATAAACTT-CA
1 TATGAAATTGTGAT-AACTTACA
13778 TATGA
1 TATGA
13783 TGAAACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (22 bp):
TATGAAATTGTGATAACTTACA
Found at i:15538 original size:21 final size:22
Alignment explanation
Indices: 15495--15544 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
15485 AAATAATGTC
*
15495 CGTAGCAAATGTAAATAAAGCT
1 CGTAGCAAATGCAAATAAAGCT
15517 CGTAGCAAATGCAAAT-AAGCT
1 CGTAGCAAATGCAAATAAAGCT
15538 CGTAGCA
1 CGTAGCA
15545 TATAGGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (22 bp):
CGTAGCAAATGCAAATAAAGCT
Done.