Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016496.1 Corchorus olitorius cultivar O-4 contig16529, 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: 116013
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:15383 original size:114 final size:115
Alignment explanation
Indices: 15183--15411 Score: 352
Period size: 114 Copynumber: 2.0 Consensus size: 115
15173 AGATTGCTAA
* *
15183 TTAATTGTGAAATGAAAATATAATAAGGTAGTTTAAATCACAAGGATCCATATTTGGTTAATAAT
1 TTAATTGTGAAATGAAAATATAAAAAGATAGTTTAAATCACAAGGATCCATATTTGGTTAATAAT
* *
15248 TTACAACTATTCTTATTTGAAAGATTG-ATCTATTGTAAGAATAAAACTC
66 TTACAAATATTCTTATTTGAAAGATTGAATATATTGTAAGAATAAAACTC
* ** * *
15297 TTAATTGTGAAATTAAAATATAAAAAGATAGTTTAAATGGCAATGATCCGTATTTGGTTAATAAT
1 TTAATTGTGAAATGAAAATATAAAAAGATAGTTTAAATCACAAGGATCCATATTTGGTTAATAAT
*
15362 TTACAAATATTCTTATTTGAAAGATTGATATATATTGTATGAATAAAACT
66 TTACAAATATTCTTATTTGAAAGATTGA-ATATATTGTAAGAATAAAACT
15412 TTCCTAATAA
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
114 84 0.82
116 19 0.18
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (115 bp):
TTAATTGTGAAATGAAAATATAAAAAGATAGTTTAAATCACAAGGATCCATATTTGGTTAATAAT
TTACAAATATTCTTATTTGAAAGATTGAATATATTGTAAGAATAAAACTC
Found at i:27517 original size:15 final size:15
Alignment explanation
Indices: 27474--27520 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
27464 TACCTTCTTG
**
27474 TTTGCATCACCCTTG
1 TTTGCATCACCCTCA
27489 TTTGCATCACCCTCA
1 TTTGCATCACCCTCA
27504 TTTGCATCACCCTCA
1 TTTGCATCACCCTCA
27519 TT
1 TT
27521 GTCTTCATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.17, C:0.36, G:0.09, T:0.38
Consensus pattern (15 bp):
TTTGCATCACCCTCA
Found at i:38453 original size:11 final size:11
Alignment explanation
Indices: 38430--38464 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
38420 TTGACAGCGT
*
38430 AACAAAAATAA
1 AACAAAAACAA
*
38441 AACGAAAACAA
1 AACAAAAACAA
38452 AACAAAAACAA
1 AACAAAAACAA
38463 AA
1 AA
38465 AACAGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:52118 original size:29 final size:29
Alignment explanation
Indices: 52065--52120 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
52055 CATGTATTGG
* **
52065 TACGGTTCCATTAACAATTGGACGGAAAT
1 TACGGTTCAATTAACAATTAAACGGAAAT
*
52094 TACGGTTCAATTAACTATTAAACGGAA
1 TACGGTTCAATTAACAATTAAACGGAA
52121 CCATACAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (29 bp):
TACGGTTCAATTAACAATTAAACGGAAAT
Found at i:76527 original size:45 final size:45
Alignment explanation
Indices: 76463--76552 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
76453 CCTCCTATTG
* *
76463 TGTAGTTCATTTCAATATCATGTTAATGAGTAGTAAAAAATAAAA
1 TGTAGTTCATTTCAATATCATGTTAATGAGTAGCAAAAAAAAAAA
76508 TGTAGTTCATTTCAATATCATGTTAATGAGTAGCAAAAAAAAAAA
1 TGTAGTTCATTTCAATATCATGTTAATGAGTAGCAAAAAAAAAAA
76553 AAAGGTAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (45 bp):
TGTAGTTCATTTCAATATCATGTTAATGAGTAGCAAAAAAAAAAA
Found at i:78353 original size:17 final size:18
Alignment explanation
Indices: 78331--78364 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
78321 ATAATTTTAC
78331 TAAAA-TAAACTAGTCAG
1 TAAAATTAAACTAGTCAG
78348 TAAAATTAAACTAGTCA
1 TAAAATTAAACTAGTCA
78365 CTTACTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (18 bp):
TAAAATTAAACTAGTCAG
Found at i:97931 original size:14 final size:15
Alignment explanation
Indices: 97888--97932 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
97878 AAAAACCCTC
97888 ATCTCC-TCTCTTCA
1 ATCTCCATCTCTTCA
*
97902 AT-TCCATCTCTGCA
1 ATCTCCATCTCTTCA
*
97916 ATCTGCAT-TCTTCA
1 ATCTCCATCTCTTCA
97930 ATC
1 ATC
97933 CTTTGTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.12
14 19 0.73
15 4 0.15
ACGTcount: A:0.20, C:0.36, G:0.04, T:0.40
Consensus pattern (15 bp):
ATCTCCATCTCTTCA
Found at i:105749 original size:29 final size:31
Alignment explanation
Indices: 105676--105749 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
105666 GACTTAAATA
* *
105676 CCAAATAAATCCCTTACCTTTTTATTTCGGG
1 CCAAATAAATCCCTGACCTATTTATTTCGGG
* *
105707 ACAAATAAATCCCTGATCTATTT-TTT-GGG
1 CCAAATAAATCCCTGACCTATTTATTTCGGG
105736 CCAAATAAATCCCT
1 CCAAATAAATCCCT
105750 CAGTTATCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 16 0.42
30 3 0.08
31 19 0.50
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.35
Consensus pattern (31 bp):
CCAAATAAATCCCTGACCTATTTATTTCGGG
Found at i:105855 original size:22 final size:22
Alignment explanation
Indices: 105827--105872 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
105817 ACGTGGCAGG
105827 TCCTTTTTTCACGGGTCGTTAC
1 TCCTTTTTTCACGGGTCGTTAC
105849 TCCTTTTTTCACGGGTCGTTAC
1 TCCTTTTTTCACGGGTCGTTAC
105871 TC
1 TC
105873 ATGTGACGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.09, C:0.28, G:0.17, T:0.46
Consensus pattern (22 bp):
TCCTTTTTTCACGGGTCGTTAC
Found at i:106885 original size:13 final size:13
Alignment explanation
Indices: 106867--106892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
106857 GGCCTGTGAA
106867 AAAAAGGACCAAC
1 AAAAAGGACCAAC
106880 AAAAAGGACCAAC
1 AAAAAGGACCAAC
106893 GTGGTAAACT
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:0.62, C:0.23, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGGACCAAC
Found at i:108999 original size:178 final size:178
Alignment explanation
Indices: 108730--109059 Score: 511
Period size: 178 Copynumber: 1.9 Consensus size: 178
108720 CCGATTAAGG
*
108730 TGATTTAAGTATCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTATCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * ** *
108795 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGTTAATGGGAATAG
66 AATTTAATGTTTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGTTAACAGAAATAG
*
108859 ACGGTCCACTTAATATTATATAACTTTTGCTTCAGTTGTCTAATTGAGA
130 ACGGTCCACTTAATATTACATAACTTTTGCTTCAGTTGTCTAATTGAGA
* * * *
108908 TGATTCAAGTGTCTCTTGAAAGTTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTATCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
*
108973 AATTTATTG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATAG
*
109037 ACGGTCTACTTAATATTACATAA
130 ACGGTCCACTTAATATTACATAA
109060 TTTACGCTTA
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
177 8 0.06
178 129 0.94
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (178 bp):
TGATTCAAGTATCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATAGA
CGGTCCACTTAATATTACATAACTTTTGCTTCAGTTGTCTAATTGAGA
Done.