Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011277.1 Corchorus olitorius cultivar O-4 contig11310, 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: 8691
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Found at i:507 original size:14 final size:15
Alignment explanation
Indices: 474--508 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
464 TTTTGCTATA
474 AAAAATATTTAAGTT
1 AAAAATATTTAAGTT
489 AAAAATATTTATA-TT
1 AAAAATATTTA-AGTT
504 AAAAA
1 AAAAA
509 AATAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
AAAAATATTTAAGTT
Found at i:1000 original size:31 final size:31
Alignment explanation
Indices: 965--1054 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
955 TCCTTTTGTG
965 CACATGGCATGCCACGTGTCACTTTTTGAAA
1 CACATGGCATGCCACGTGTCACTTTTTGAAA
* * **
996 CACATGACATACCACGTGTCACTTTTTGGTA
1 CACATGGCATGCCACGTGTCACTTTTTGAAA
* * **
1027 TACATGGCGTGATACGTGTCACTTTTTG
1 CACATGGCATGCCACGTGTCACTTTTTG
1055 GTATATGTGA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (31 bp):
CACATGGCATGCCACGTGTCACTTTTTGAAA
Found at i:5729 original size:22 final size:22
Alignment explanation
Indices: 5700--5835 Score: 132
Period size: 22 Copynumber: 6.2 Consensus size: 22
5690 TTGCTATATT
*
5700 ATTTTGATAACCTCTCTAAGAA
1 ATTTTGATAACCTCTCTATGAA
* *
5722 ATTATGATAACCTCTCTGTGAA
1 ATTTTGATAACCTCTCTATGAA
* * * *
5744 ACTTTGATAACCACACTATTAA
1 ATTTTGATAACCTCTCTATGAA
5766 ATTTTGAT-ACCATC-CTATGAA
1 ATTTTGATAACC-TCTCTATGAA
** * *
5787 ATTTTGATAACAACACTATAAA
1 ATTTTGATAACCTCTCTATGAA
* *
5809 ATTGTGATAACCTCTATATGAA
1 ATTTTGATAACCTCTCTATGAA
5831 ATTTT
1 ATTTT
5836 TTTTGATGAC
Statistics
Matches: 89, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
21 18 0.20
22 71 0.80
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
ATTTTGATAACCTCTCTATGAA
Found at i:5803 original size:43 final size:44
Alignment explanation
Indices: 5720--5835 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 44
5710 CCTCTCTAAG
* * * * * *
5720 AAATTATGATAACCTCTCTGTGAAACTTTGATAACCACACTATT
1 AAATTGTGATAACCTCTATATGAAATTTTGATAACAACACTATA
* *
5764 AAATTTTGAT-ACCATC-CTATGAAATTTTGATAACAACACTATA
1 AAATTGTGATAACC-TCTATATGAAATTTTGATAACAACACTATA
5807 AAATTGTGATAACCTCTATATGAAATTTT
1 AAATTGTGATAACCTCTATATGAAATTTT
5836 TTTTGATGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
43 37 0.60
44 25 0.40
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (44 bp):
AAATTGTGATAACCTCTATATGAAATTTTGATAACAACACTATA
Found at i:5946 original size:22 final size:22
Alignment explanation
Indices: 5897--6115 Score: 137
Period size: 22 Copynumber: 10.0 Consensus size: 22
5887 TGATTTGGTA
*
5897 CACTATGAAATTTGGATAACCAT
1 CACTATGAAATTTTGATAACC-T
5920 -ACTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCT
* * *
5941 CCCTAT-AGAATGTTGATAACTTT
1 CACTATGA-AATTTTGATAAC-CT
* *
5964 C-CTAT-AGAATTTCGTTAACCT
1 CACTATGA-AATTTTGATAACCT
** *
5985 CTTTATGAAATTTTGATAAGCAT
1 CACTATGAAATTTTGATAA-CCT
* *
6008 -AATATGAAATTTTGATTACCT
1 CACTATGAAATTTTGATAACCT
** *
6029 -TTTATGAAATTTTTG-TAACCA
1 CACTATGAAA-TTTTGATAACCT
* * *
6050 CATTATGTAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCT
* * **
6072 CATTATGAAATTTTGATAGCAG
1 CACTATGAAATTTTGATAACCT
*
6094 CACTATGAAATTTCGATAACCT
1 CACTATGAAATTTTGATAACCT
6116 GCAAAGTTCA
Statistics
Matches: 156, Mismatches: 31, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
21 22 0.14
22 129 0.83
23 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCT
Found at i:6019 original size:44 final size:44
Alignment explanation
Indices: 5971--6115 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 44
5961 TTTCCTATAG
* *
5971 AATTTCGTTAACCTCTTTATGAAATTTTGATAAGCATAATATGA
1 AATTTCGATAACCTCTTTATGAAATTTTGATAAGCACAATATGA
* * * * *
6015 AATTTTGATTACCT-TTTATGAAATTTTTG-TAACCACATTATGT
1 AATTTCGATAACCTCTTTATGAAA-TTTTGATAAGCACAATATGA
* * * *
6058 AATTTTGATAACCACATTATGAAATTTTGAT-AGCAGCACTATGA
1 AATTTCGATAACCTCTTTATGAAATTTTGATAAGCA-CAATATGA
6102 AATTTCGATAACCT
1 AATTTCGATAACCT
6116 GCAAAGTTCA
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
43 39 0.48
44 43 0.52
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (44 bp):
AATTTCGATAACCTCTTTATGAAATTTTGATAAGCACAATATGA
Found at i:6040 original size:43 final size:43
Alignment explanation
Indices: 5979--6115 Score: 143
Period size: 43 Copynumber: 3.1 Consensus size: 43
5969 AGAATTTCGT
*
5979 TAACCTCTTTATGAAATTTTGATAAGCATAATATGAAATTTTGA
1 TAACCT-TTTATGAAATTTTGATAAGCACAATATGAAATTTTGA
* * * *
6023 TTACCTTTTATGAAATTTTTG-TAACCACATTATGTAATTTTGA
1 TAACCTTTTATGAAA-TTTTGATAAGCACAATATGAAATTTTGA
** * *
6066 TAACCACATTATGAAATTTTGAT-AGCAGCACTATGAAATTTCGA
1 TAACC-TTTTATGAAATTTTGATAAGCA-CAATATGAAATTTTGA
6110 TAACCT
1 TAACCT
6116 GCAAAGTTCA
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
43 39 0.51
44 37 0.49
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (43 bp):
TAACCTTTTATGAAATTTTGATAAGCACAATATGAAATTTTGA
Found at i:7402 original size:22 final size:22
Alignment explanation
Indices: 7377--7424 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
7367 TAAAAAAATT
7377 ATAGGG-AGATTAACAAAATCTC
1 ATAGGGAAGATT-ACAAAATCTC
* *
7399 ATAGGGAAGGTTACAAAATTTC
1 ATAGGGAAGATTACAAAATCTC
7421 ATAG
1 ATAG
7425 TTAGGTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (22 bp):
ATAGGGAAGATTACAAAATCTC
Found at i:8603 original size:29 final size:28
Alignment explanation
Indices: 8559--8614 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
8549 TTCTTCAAAC
*
8559 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
8587 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
8615 GTGGAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Done.