Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011305.1 Corchorus olitorius cultivar O-4 contig11338, 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: 17783
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:284 original size:26 final size:26
Alignment explanation
Indices: 246--305 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
236 AGGTATTCCA
246 TCTTTT-C-CTTTGCCCTTAATGTCT
1 TCTTTTGCACTTTGCCCTTAATGTCT
270 TCTTTTGCACTTTGCCCTTAATGTCT
1 TCTTTTGCACTTTGCCCTTAATGTCT
296 TCTTTTGCAC
1 TCTTTTGCAC
306 AAGAGTCTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 6 0.18
25 1 0.03
26 27 0.79
ACGTcount: A:0.10, C:0.28, G:0.10, T:0.52
Consensus pattern (26 bp):
TCTTTTGCACTTTGCCCTTAATGTCT
Found at i:1461 original size:13 final size:13
Alignment explanation
Indices: 1443--1468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1433 TATATAATGA
1443 AGACCAGAAACCC
1 AGACCAGAAACCC
1456 AGACCAGAAACCC
1 AGACCAGAAACCC
1469 TCTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.38, G:0.15, T:0.00
Consensus pattern (13 bp):
AGACCAGAAACCC
Found at i:1992 original size:28 final size:28
Alignment explanation
Indices: 1947--2156 Score: 330
Period size: 28 Copynumber: 7.5 Consensus size: 28
1937 AGTGCACTCG
* * *
1947 AAATGACCAGAATACCCCTGGACATGTA
1 AAATGACCAAAATGCCCCTGGACATGAA
*
1975 AATTGACCAAAATGCCCCTGGACATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
*
2003 AAATGACCAAAATGCCCCTGGACATGAC
1 AAATGACCAAAATGCCCCTGGACATGAA
*
2031 AAATGACCAAAATGCCCCTCGACATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
*
2059 AAATGACCAAAATGCCCCAGGACATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
* *
2087 AAATGACCAAAATACCCTTGGACATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
*
2115 AAATGACCAAAATGCCCCAGGACATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
2143 AAATGACCAAAATG
1 AAATGACCAAAATG
2157 AGAAGTAAAT
Statistics
Matches: 166, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 166 1.00
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGAA
Found at i:2615 original size:2 final size:2
Alignment explanation
Indices: 2571--2601 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2561 GGAATAATAA
*
2571 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2602 AGTTGTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3834 original size:1 final size:1
Alignment explanation
Indices: 3828--3856 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
3818 TGTAATTTGG
3828 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3857 CATTTTCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5154 original size:40 final size:40
Alignment explanation
Indices: 5099--5176 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
5089 TGCAAATTTG
5099 TTTAGCTATGACATACAAGTAGTTTATATGCCAATTGCTC
1 TTTAGCTATGACATACAAGTAGTTTATATGCCAATTGCTC
5139 TTTAGCTATGACATACAAGTAGTTTATATGCCAATTGC
1 TTTAGCTATGACATACAAGTAGTTTATATGCCAATTGC
5177 CAAAGCATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (40 bp):
TTTAGCTATGACATACAAGTAGTTTATATGCCAATTGCTC
Found at i:10050 original size:29 final size:29
Alignment explanation
Indices: 10017--10128 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 29
10007 GTTACGACTG
10017 CCAGTGGAACCCGTACGTAGTGAATAATA
1 CCAGTGGAACCCGTACGTAGTGAATAATA
10046 CCAGTGGAACCCGTACGTAGTGAATAAGTTACGA
1 CCAGTGGAACCCGTACGTAGTGAATAA--T---A
*
10080 CTGCCAGTGGAACCCGTACGTAGTGAATAATG
1 ---CCAGTGGAACCCGTACGTAGTGAATAATA
*
10112 CCAGTGGAACCTGTACG
1 CCAGTGGAACCCGTACG
10129 GAGTAAGCTG
Statistics
Matches: 73, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
29 43 0.59
31 1 0.01
34 1 0.01
35 1 0.01
37 27 0.37
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (29 bp):
CCAGTGGAACCCGTACGTAGTGAATAATA
Found at i:10109 original size:66 final size:66
Alignment explanation
Indices: 10003--10128 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
9993 AAACGAACGG
10003 ATAAGTTACGACTGCCAGTGGAACCCGTACGTAGTGAATAATACCAGTGGAACCCGTACGTAGTG
1 ATAAGTTACGACTGCCAGTGGAACCCGTACGTAGTGAATAATACCAGTGGAACCCGTACGTAGTG
10068 A
66 A
* *
10069 ATAAGTTACGACTGCCAGTGGAACCCGTACGTAGTGAATAATGCCAGTGGAACCTGTACG
1 ATAAGTTACGACTGCCAGTGGAACCCGTACGTAGTGAATAATACCAGTGGAACCCGTACG
10129 GAGTAAGCTG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (66 bp):
ATAAGTTACGACTGCCAGTGGAACCCGTACGTAGTGAATAATACCAGTGGAACCCGTACGTAGTG
A
Done.