Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016051.1 Corchorus olitorius cultivar O-4 contig16084, 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: 41658
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:6720 original size:76 final size:76
Alignment explanation
Indices: 6568--6720 Score: 164
Period size: 76 Copynumber: 2.0 Consensus size: 76
6558 GGACAAGGGC
* * * * * *
6568 CCCGACTCCTCCTGGGCGCCCACATGGTTGCCTTGAGCATACATGTGGTTTGCCTTAAGACCTAG
1 CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACACATGTGATTTGCCTGAACACCCAG
*
6633 CTGGGCAGTGT
66 CTAGGCAGTGT
* * * * *
6644 CCCGACTCCACCTGGGTGCCCACATGGTTTGTC-TGAGGACCCATGTGATTTGCCTGATCACCCA
1 CCCGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAGCACACATGTGATTTGCCTGAACACCCA
* *
6708 GGTAGGCTGTGT
65 GCTAGGCAGTGT
6720 C
1 C
6721 ATGGCTCGGT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
76 58 0.94
77 4 0.06
ACGTcount: A:0.16, C:0.31, G:0.27, T:0.26
Consensus pattern (76 bp):
CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACACATGTGATTTGCCTGAACACCCAG
CTAGGCAGTGT
Found at i:14685 original size:127 final size:127
Alignment explanation
Indices: 14450--14692 Score: 274
Period size: 127 Copynumber: 1.9 Consensus size: 127
14440 ATATGCAATA
* *
14450 ATAGAGAAAGCACAAACATCATAAACCGTATTTCCTAAATAAGAATCCGAGTCTAAATCAATATT
1 ATAGAGAAAGAACAAACATCATAAACCCTATTTCCTAAATAAGAATCCGAGTCTAAATCAATATT
* *** ** * * *
14515 AACAAACAAACACGGCAAAAGATTTTTTTTTAATAGCGCTTTATTGAAAGCAACATACACAT
66 AACAAACAAACACAGCAAAAGAGAGTTTTCCAACAACACTTTATTGAAAGCAACATACACAT
* * * *
14577 ATAGAGAAAGAACAAATATCATAAACCCTATTTTCTGAATAAGAAT-CGAAGTGTAAATCAATAT
1 ATAGAGAAAGAACAAACATCATAAACCCTATTTCCTAAATAAGAATCCG-AGTCTAAATCAATAT
** * * *
14641 TAA-AGAACAAACACAGCAAGGGAGAGTTTTCCCACAACATTTTATTGGAAGC
65 TAACA-AACAAACACAGCAAAAGAGAGTTTTCCAACAACACTTTATTGAAAGC
14693 TAATACATAT
Statistics
Matches: 94, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
126 3 0.03
127 91 0.97
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (127 bp):
ATAGAGAAAGAACAAACATCATAAACCCTATTTCCTAAATAAGAATCCGAGTCTAAATCAATATT
AACAAACAAACACAGCAAAAGAGAGTTTTCCAACAACACTTTATTGAAAGCAACATACACAT
Found at i:24931 original size:30 final size:30
Alignment explanation
Indices: 24873--25074 Score: 263
Period size: 30 Copynumber: 6.9 Consensus size: 30
24863 CCCCTAGACG
* *
24873 TGCAAAA-TGACCAAAATG-CCCCTAGATA
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
24901 TGCAAAAGTGACTAAAATGTCCCCTGGATA
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
* **
24931 TGCAAAAGTGACTAGAATGTCCCCTGGACG
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
* *
24961 TGCAAAA-TGACCAAAATG-CCCCTAGATA
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
24989 TGCAAAAGTGACTAAAATGTCCCCTGGATA
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
* **
25019 TGCAAAAGTGACTAGAATGTCCCCTGGACG
1 TGCAAAAGTGACTAAAATGTCCCCTGGATA
*
25049 TGCAAAA-TGACCAAAATG-CCCCTGGA
1 TGCAAAAGTGACTAAAATGTCCCCTGGA
25075 CATGAATAAT
Statistics
Matches: 153, Mismatches: 17, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
28 29 0.19
29 38 0.25
30 86 0.56
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (30 bp):
TGCAAAAGTGACTAAAATGTCCCCTGGATA
Found at i:24935 original size:58 final size:60
Alignment explanation
Indices: 24873--25074 Score: 263
Period size: 58 Copynumber: 3.5 Consensus size: 60
24863 CCCCTAGACG
*
24873 TGCAAAA-TGACCAAAATG-CCCCTAGATATGCAAAAGTGACTAAAATGTCCCCTGGATA
1 TGCAAAAGTGACCAAAATGTCCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATA
* * ** * *
24931 TGCAAAAGTGACTAGAATGTCCCCTGGACGTGCAAAA-TGACCAAAATG-CCCCTAGATA
1 TGCAAAAGTGACCAAAATGTCCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATA
* * **
24989 TGCAAAAGTGACTAAAATGTCCCCTGGATATGCAAAAGTGACTAGAATGTCCCCTGGACG
1 TGCAAAAGTGACCAAAATGTCCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATA
25049 TGCAAAA-TGACCAAAATG-CCCCTGGA
1 TGCAAAAGTGACCAAAATGTCCCCTGGA
25075 CATGAATAAT
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
58 58 0.47
59 38 0.31
60 28 0.23
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (60 bp):
TGCAAAAGTGACCAAAATGTCCCCTGGATATGCAAAAGTGACTAAAATGTCCCCTGGATA
Found at i:24968 original size:88 final size:88
Alignment explanation
Indices: 24863--25071 Score: 409
Period size: 88 Copynumber: 2.4 Consensus size: 88
24853 GACCAAAATA
*
24863 CCCCTAGACGTGCAAAATGACCAAAATGCCCCTAGATATGCAAAAGTGACTAAAATGTCCCCTGG
1 CCCCTGGACGTGCAAAATGACCAAAATGCCCCTAGATATGCAAAAGTGACTAAAATGTCCCCTGG
24928 ATATGCAAAAGTGACTAGAATGT
66 ATATGCAAAAGTGACTAGAATGT
24951 CCCCTGGACGTGCAAAATGACCAAAATGCCCCTAGATATGCAAAAGTGACTAAAATGTCCCCTGG
1 CCCCTGGACGTGCAAAATGACCAAAATGCCCCTAGATATGCAAAAGTGACTAAAATGTCCCCTGG
25016 ATATGCAAAAGTGACTAGAATGT
66 ATATGCAAAAGTGACTAGAATGT
25039 CCCCTGGACGTGCAAAATGACCAAAATGCCCCT
1 CCCCTGGACGTGCAAAATGACCAAAATGCCCCT
25072 GGACATGAAT
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 120 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (88 bp):
CCCCTGGACGTGCAAAATGACCAAAATGCCCCTAGATATGCAAAAGTGACTAAAATGTCCCCTGG
ATATGCAAAAGTGACTAGAATGT
Found at i:30848 original size:27 final size:27
Alignment explanation
Indices: 30818--30888 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
30808 TGTGAACTTA
*
30818 AAATGACCAAAATGCCCATGAATGTGC
1 AAATGACCAAAATGCCCATGAACGTGC
* *
30845 AAATGACCAAAATGCCCTTGGACGTGC
1 AAATGACCAAAATGCCCATGAACGTGC
*
30872 AAATGACTAAAATGCCC
1 AAATGACCAAAATGCCC
30889 CTAGGTGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCATGAACGTGC
Found at i:40919 original size:253 final size:253
Alignment explanation
Indices: 40471--40972 Score: 914
Period size: 253 Copynumber: 2.0 Consensus size: 253
40461 AATTTCTTGA
**
40471 GGTAAAAGTACCCGGGAGGTCCCTGTACTATATGAAATGTTGATTTTGGTCCCTATACTTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACAAAATGTTGATTTTGGTCCCTATACTTTTTTT
* * **
40536 TTCTACAAATTCGTCTCTCTACTATCAGAACCTATCGCCCGAGATCCCTCACGTTAGTGTGTCGT
66 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGATCCCTCACGTTAGCATGTCGT
*
40601 GACAGACCCGTCAAATCTGCTGACGTGGCACTAACACCGTCTTTTTTTGCTGACGTGGCAGGTGA
131 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTTGCTGACGTGGCAGGTGA
*
40666 CACGTGGAATAAAAATTAAGTATATTTTTAATATATTTTATTTTATTGAAATTTATTT
196 CACGTGGAATAAAAATTAAATATATTTTTAATATATTTTATTTTATTGAAATTTATTT
*
40724 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACAAAATGTTGATTTTGGTCCCTGTACTTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACAAAATGTTGATTTTGGTCCCTATACTTTTTTT
40789 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGATCCCTCACGTTAGCATGTCGT
66 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGATCCCTCACGTTAGCATGTCGT
40854 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTTGCTGACGTGGCAGGTGA
131 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTTGCTGACGTGGCAGGTGA
*
40919 CACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTT
196 CACGTGGAATAAAAATTAAATATATTTTTAATATATTTTATTTTATTGAAATTT
40973 TTTTTTAAAA
Statistics
Matches: 239, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
253 239 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (253 bp):
GGTAAAAGTACCCGGGAGGTCCCTGTACTATACAAAATGTTGATTTTGGTCCCTATACTTTTTTT
TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGATCCCTCACGTTAGCATGTCGT
GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTTGCTGACGTGGCAGGTGA
CACGTGGAATAAAAATTAAATATATTTTTAATATATTTTATTTTATTGAAATTTATTT
Done.