Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017843.1 Corchorus olitorius cultivar O-4 contig17876, 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: 54086
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:3174 original size:114 final size:114
Alignment explanation
Indices: 2969--3193 Score: 369
Period size: 114 Copynumber: 2.0 Consensus size: 114
2959 TAACACGTGC
*
2969 TGTAGATGTCCTCGTATAAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTCCTCGTCG
1 TGTAGATGTCCTCATATAAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTCCTCGTCG
* ** *
3034 TGACCCTTTAACGAATAACGTTGGTACCAAATTATCAAACTATTCTTTT
66 TGACCCTTTAACGAAAAACGGCGGTACCAAATCATCAAACTATTCTTTT
* * * *
3083 TGTAGATGTCTTCATATAAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTTCTTGTTG
1 TGTAGATGTCCTCATATAAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTCCTCGTCG
3148 TGACCCTTTAACGAAAAACGGCGGTACCAAATCATCAAACTATTCT
66 TGACCCTTTAACGAAAAACGGCGGTACCAAATCATCAAACTATTCT
3194 ATTACGTAAT
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (114 bp):
TGTAGATGTCCTCATATAAAGAATCTTCATTTTGTCGTGTTATTATGGGTTGTTTGTCCTCGTCG
TGACCCTTTAACGAAAAACGGCGGTACCAAATCATCAAACTATTCTTTT
Found at i:6150 original size:32 final size:32
Alignment explanation
Indices: 6114--6220 Score: 83
Period size: 32 Copynumber: 3.2 Consensus size: 32
6104 AATAAGCGAC
6114 CTAAACCGATACCGTTTTACCAGAAAAACCTG
1 CTAAACCGATACCGTTTTACCAGAAAAACCTG
* **
6146 CTAAAATAAAACCGATACCGTTTTACCACCAAGAAA--AA
1 C-----T-AAACCGATACCGTTTTACCA-GAA-AAACCTG
**
6184 AAAAACCGATACCGTTTTACCAGAAAAACCTG
1 CTAAACCGATACCGTTTTACCAGAAAAACCTG
6216 CTAAA
1 CTAAA
6221 ATAAAACCGA
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
30 3 0.05
31 2 0.04
32 24 0.44
37 1 0.02
38 20 0.36
39 2 0.04
40 3 0.05
ACGTcount: A:0.45, C:0.25, G:0.10, T:0.20
Consensus pattern (32 bp):
CTAAACCGATACCGTTTTACCAGAAAAACCTG
Found at i:6167 original size:38 final size:38
Alignment explanation
Indices: 6116--6243 Score: 180
Period size: 38 Copynumber: 3.5 Consensus size: 38
6106 TAAGCGACCT
6116 AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATA
1 AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATA
* *
6154 AAACCGATACCGTTTTACCACCAAGAA------AAAA-A
1 AAACCGATACCGTTTTACCA-GAAAAACCTGCTAAAATA
6186 AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATA
1 AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATA
6224 AAACCGATACCGTTTTACCA
1 AAACCGATACCGTTTTACCA
6244 CCAAGAAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
31 4 0.05
32 21 0.27
33 4 0.05
37 4 0.05
38 41 0.53
39 4 0.05
ACGTcount: A:0.45, C:0.25, G:0.10, T:0.20
Consensus pattern (38 bp):
AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATA
Found at i:6203 original size:70 final size:68
Alignment explanation
Indices: 6116--6268 Score: 288
Period size: 70 Copynumber: 2.2 Consensus size: 68
6106 TAAGCGACCT
6116 AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATAAAACCGATACCGTTTTACCACCAAGAA
1 AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATAAAACCGATACCGTTTTACCACCAAG--
6181 AAAAA
64 AAAAA
6186 AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATAAAACCGATACCGTTTTACCACCAAGAA
1 AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATAAAACCGATACCGTTTTACCACCAAGAA
6251 AAA
66 AAA
6254 AAACCGATACCGTTT
1 AAACCGATACCGTTT
6269 GGCTTCTGTT
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
68 20 0.24
70 63 0.76
ACGTcount: A:0.45, C:0.25, G:0.10, T:0.20
Consensus pattern (68 bp):
AAACCGATACCGTTTTACCAGAAAAACCTGCTAAAATAAAACCGATACCGTTTTACCACCAAGAA
AAA
Found at i:10607 original size:30 final size:30
Alignment explanation
Indices: 10573--10634 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
10563 ATTTTTATCT
10573 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
* *
10603 TGACTTTTCTCTTATATCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
10633 TG
1 TG
10635 GCTTATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.47
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:52135 original size:31 final size:31
Alignment explanation
Indices: 52060--52135 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
52050 TGCTGAATAC
*
52060 CACGTCGGACCAAAAATGACACATGGCAATGT
1 CACGTCAGACC-AAAATGACACATGGCAATGT
* * **
52092 CACGTTATACCAAAATGACATGTGGCAATG-
1 CACGTCAGACCAAAATGACACATGGCAATGT
52122 CTACGTCAGACCAA
1 C-ACGTCAGACCAA
52136 GTCACTGACG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 1 0.03
31 27 0.75
32 8 0.22
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (31 bp):
CACGTCAGACCAAAATGACACATGGCAATGT
Found at i:53165 original size:21 final size:21
Alignment explanation
Indices: 53139--53180 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
53129 GGATAATGGA
53139 ACCCCAAGAACCACCATTTCT
1 ACCCCAAGAACCACCATTTCT
*
53160 ACCCCAAGGACCACCATTTCT
1 ACCCCAAGAACCACCATTTCT
53181 TCCATCGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.43, G:0.07, T:0.19
Consensus pattern (21 bp):
ACCCCAAGAACCACCATTTCT
Done.