Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021546.1 Corchorus olitorius cultivar O-4 contig21579, 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: 12245
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Found at i:3129 original size:16 final size:17
Alignment explanation
Indices: 3108--3139 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3098 GAGATTGCGT
3108 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
3124 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
3140 GCACTTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Found at i:10645 original size:39 final size:39
Alignment explanation
Indices: 10047--10645 Score: 519
Period size: 39 Copynumber: 15.4 Consensus size: 39
10037 TTTCGTGGCC
* * *
10047 TAGAGTTT-CGTTTAATTAAACCTGCTTAGGTCTCTGTT
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* * * * * * **
10085 TAGAATTTTCATTTAATTGAACCTACCTAGGTCTCCGTT
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* * * **
10124 TAGAATTTTCATTTGAGTAAACCTGCTTAGGTCTCTGCT
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* * *
10163 TATAGTTT-CGTTTAAGGAAACCTGCTTAGGTCTCTATT
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* ** ** * * * **
10201 AAGTTTTTTTATTTAAGTAAACATGTTTAGGCCTCTGCT
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* * *
10240 TAAAGTTT-CGTTTAAGTAAACCTGCTTAGGTCTCTGTT
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* * * *
10278 TAGAATTTTCGTTTAAGTAAACCTGCTTAAGTCTCTATT
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* **
10317 TAGAGTTGT-CATTTAAGTAAACCTGCTTAGGCCTCTGCT
1 TAGAGTT-TCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* * *
10356 CAGAGTTT-CGTTTAAGAAAAACCTGCTTAGGTCTCTATT
1 TAGAGTTTCCATTTAAG-TAAACCTGCTTAGGTCTCTATT
* * * * *
10395 TA-AATTAACCATTTAAGTAAACCCGCTTAGGTCCCTGTT
1 TAGAGTT-TCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* * * * *
10434 TAAAGTTTCCATTCAAGTAAACCTGCTTAGGTCTATGTC
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* * * *
10473 TAAAGTTTCCATTTAAGTAAACCTGCTTAGGTCTGTGTC
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* * * *
10512 TAAAGTTTCCAATTAAGTAAACCTGCCTAGATCTCTATT
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
10551 TAGAG-TTCCATTTTAAGTAAACCTGCTTAGGTCTCTATT
1 TAGAGTTTCCA-TTTAAGTAAACCTGCTTAGGTCTCTATT
* ** *
10590 TATAGTTTCCATTTAAGTAAATTTGCTTAGATCTCTATT
1 TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
* *
10629 TAGAGTTTTCGTTTAAG
1 TAGAGTTTCCATTTAAG
10646 AAAAAACCTG
Statistics
Matches: 459, Mismatches: 92, Indels: 19
0.81 0.16 0.03
Matches are distributed among these distances:
38 82 0.18
39 361 0.79
40 16 0.03
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (39 bp):
TAGAGTTTCCATTTAAGTAAACCTGCTTAGGTCTCTATT
Found at i:10645 original size:117 final size:115
Alignment explanation
Indices: 10047--10645 Score: 574
Period size: 117 Copynumber: 5.1 Consensus size: 115
10037 TTTCGTGGCC
* * * * * *
10047 TAGAG-TTTCGTTTAATTAAACCTGCTTAGGTCTCTGTTTAGAATTTTCATTTAATTGAACCTAC
1 TAGAGTTTTCGTTTAAGTAAACCTGCTTAGGTCTCTATTTAG-AGTTTCATTTAAGTAAACCTGC
* * * * *
10111 CTAGGTCTCCGTTTAGAATTTTCATTTGAGTAAACCTGCTTAGGTCTCTGCT
65 TTAGGTCTCTGTTTA-AAGTTTCATTTAAGTAAACCTGCTTAGGTCTCTGTT
* * * ** * * *
10163 TATAG-TTTCGTTTAAGGAAACCTGCTTAGGTCTCTATTAAGTTTTTTTATTTAAGTAAACATGT
1 TAGAGTTTTCGTTTAAGTAAACCTGCTTAGGTCTCTATTTAG-AGTTTCATTTAAGTAAACCTGC
* * *
10227 TTAGGCCTCTGCTTAAAGTTTCGTTTAAGTAAACCTGCTTAGGTCTCTGTT
65 TTAGGTCTCTGTTTAAAGTTTCATTTAAGTAAACCTGCTTAGGTCTCTGTT
* *
10278 TAGAATTTTCGTTTAAGTAAACCTGCTTAAGTCTCTATTTAGAGTTGTCATTTAAGTAAACCTGC
1 TAGAGTTTTCGTTTAAGTAAACCTGCTTAGGTCTCTATTTAGAGTT-TCATTTAAGTAAACCTGC
* * * * * * *
10343 TTAGGCCTCTGCTCAGAGTTTCGTTTAAGAAAAACCTGCTTAGGTCTCTATT
65 TTAGGTCTCTGTTTAAAGTTTCATTTAAG-TAAACCTGCTTAGGTCTCTGTT
* ** * * * * * *
10395 TA-AATTAACCATTTAAGTAAACCCGCTTAGGTCCCTGTTTAAAGTTTCCATTCAAGTAAACCTG
1 TAGAGTT-TTCGTTTAAGTAAACCTGCTTAGGTCTCTATTTAGAGTTT-CATTTAAGTAAACCTG
* * * *
10459 CTTAGGTCTATGTCTAAAGTTTCCATTTAAGTAAACCTGCTTAGGTCTGTGTC
64 CTTAGGTCTCTGTTTAAAGTTT-CATTTAAGTAAACCTGCTTAGGTCTCTGTT
* * ** * * *
10512 TAAAGTTTCCAATTAAGTAAACCTGCCTAGATCTCTATTTAGAGTTCCATTTTAAGTAAACCTGC
1 TAGAGTTTTCGTTTAAGTAAACCTGCTTAGGTCTCTATTTAGAGTTTCA-TTTAAGTAAACCTGC
* * ** * *
10577 TTAGGTCTCTATTTATAGTTTCCATTTAAGTAAATTTGCTTAGATCTCTATT
65 TTAGGTCTCTGTTTAAAGTTT-CATTTAAGTAAACCTGCTTAGGTCTCTGTT
10629 TAGAGTTTTCGTTTAAG
1 TAGAGTTTTCGTTTAAG
10646 AAAAAACCTG
Statistics
Matches: 395, Mismatches: 80, Indels: 15
0.81 0.16 0.03
Matches are distributed among these distances:
115 37 0.09
116 144 0.36
117 204 0.52
118 10 0.03
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (115 bp):
TAGAGTTTTCGTTTAAGTAAACCTGCTTAGGTCTCTATTTAGAGTTTCATTTAAGTAAACCTGCT
TAGGTCTCTGTTTAAAGTTTCATTTAAGTAAACCTGCTTAGGTCTCTGTT
Found at i:10665 original size:25 final size:25
Alignment explanation
Indices: 10631--10680 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
10621 TCTCTATTTA
10631 GAGTTTTCGTTTAAGAAAAAACCTG
1 GAGTTTTCGTTTAAGAAAAAACCTG
10656 GAGTTTTCGTTTAAGAAAAAACCTG
1 GAGTTTTCGTTTAAGAAAAAACCTG
10681 TTTAGGATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (25 bp):
GAGTTTTCGTTTAAGAAAAAACCTG
Done.