Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013660.1 Corchorus olitorius cultivar O-4 contig13693, 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: 24894
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:197 original size:17 final size:16
Alignment explanation
Indices: 156--198 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
146 AAGCTGCCAT
156 ATCTTCTTCCTCGCAC
1 ATCTTCTTCCTCGCAC
* *
172 TTCTCTCTTCCTCGGCTC
1 ATCT-TCTTCCTC-GCAC
190 ATCTTCTTC
1 ATCTTCTTC
199 GACGGCAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 6 0.27
ACGTcount: A:0.07, C:0.42, G:0.07, T:0.44
Consensus pattern (16 bp):
ATCTTCTTCCTCGCAC
Found at i:2065 original size:27 final size:28
Alignment explanation
Indices: 2035--2109 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
2025 AGTGAACCTA
2035 AAATGACCAAAATGCCCCTGAA-CGTGC
1 AAATGACCAAAATGCCCCTGAATCGTGC
* ** *
2062 AAATGACCAAAATGCTCCTGAATTTTTGG
1 AAATGACCAAAATGCCCCTGAA-TCGTGC
2091 AAATGACCAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
2110 AGGTGATCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 21 0.51
29 20 0.49
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.21
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGAATCGTGC
Found at i:5679 original size:29 final size:29
Alignment explanation
Indices: 5639--5700 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
5629 AACTAATTTA
* * *
5639 GTTTCTTTTATTTGTTTGAGCAATTTTTT
1 GTTTCTTCTATTTGTTTGAGCAAGTTTCT
5668 GTTTCTTCTATTTGTTTGAGCAAGTTTCT
1 GTTTCTTCTATTTGTTTGAGCAAGTTTCT
5697 GTTT
1 GTTT
5701 ATTTTAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.13, C:0.10, G:0.16, T:0.61
Consensus pattern (29 bp):
GTTTCTTCTATTTGTTTGAGCAAGTTTCT
Found at i:7307 original size:29 final size:29
Alignment explanation
Indices: 7272--7339 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
7262 TAACTAATTA
* *
7272 GTTTCTTTTATTTGTTTGAGCAATTTTTT
1 GTTTCTTTTATTTGTTTGAGCAAGTTTTC
*
7301 GTTTCTTCTATTTGTTTGAGCAAGTTTTC
1 GTTTCTTTTATTTGTTTGAGCAAGTTTTC
*
7330 GTTTATTTTA
1 GTTTCTTTTA
7340 ATAAGTAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.62
Consensus pattern (29 bp):
GTTTCTTTTATTTGTTTGAGCAAGTTTTC
Found at i:8934 original size:29 final size:29
Alignment explanation
Indices: 8899--8966 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
8889 TAGCTAATTA
* *
8899 GTTTCTTTTATTTGTTTGAGCAATTTTTT
1 GTTTCTTTTATTTGTTTGAGCAAGTTTCT
*
8928 GTTTCTTCTATTTGTTTGAGCAAGTTTCT
1 GTTTCTTTTATTTGTTTGAGCAAGTTTCT
*
8957 GTTTATTTTA
1 GTTTCTTTTA
8967 ATTAGTAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.62
Consensus pattern (29 bp):
GTTTCTTTTATTTGTTTGAGCAAGTTTCT
Found at i:22544 original size:42 final size:43
Alignment explanation
Indices: 22476--22562 Score: 140
Period size: 42 Copynumber: 2.0 Consensus size: 43
22466 GTTTTAAATA
* * *
22476 TTTTTTTGGTTTTTTACATGTAAAATTTTTTTAGTAGCTAACT
1 TTTTTTTGGATTTTTACATGTAAAATTTTTTTAGCAGCCAACT
22519 TTTTTTTGGATTTTTACATGT-AAATTTTTTTAGCAGCCAACT
1 TTTTTTTGGATTTTTACATGTAAAATTTTTTTAGCAGCCAACT
22561 TT
1 TT
22563 ATGTAAGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 21 0.51
43 20 0.49
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.56
Consensus pattern (43 bp):
TTTTTTTGGATTTTTACATGTAAAATTTTTTTAGCAGCCAACT
Found at i:23824 original size:19 final size:19
Alignment explanation
Indices: 23806--23842 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23796 TATTAATTAT
*
23806 TTTA-ATATTATATTTTTA
1 TTTATATATTACATTTTTA
23824 TTTATATATTACATTTTTA
1 TTTATATATTACATTTTTA
23843 CATAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTACATTTTTA
Found at i:24128 original size:11 final size:11
Alignment explanation
Indices: 24114--24138 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24104 TATGTAAGAT
24114 ATATAATAATA
1 ATATAATAATA
24125 ATATAATAATA
1 ATATAATAATA
24136 ATA
1 ATA
24139 ATAAAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAATAATA
Found at i:24135 original size:14 final size:13
Alignment explanation
Indices: 24112--24141 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
24102 AATATGTAAG
24112 ATATATAATAATA
1 ATATATAATAATA
24125 ATATAATAATAATA
1 ATAT-ATAATAATA
24139 ATA
1 ATA
24142 AAATTTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATATAATAATA
Done.