Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018622.1 Corchorus olitorius cultivar O-4 contig18655, 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: 23126
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7094 original size:44 final size:44
Alignment explanation
Indices: 7040--7129 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
7030 GACTTTGATG
* *
7040 GGGCTATGGAAGCT-AGAGAGGACTTTGTTGGGGATTTAGAAGCT
1 GGGCTATGGAAGATGAGA-AGGACTTTGCTGGGGATTTAGAAGCT
* * * *
7084 GGGCTTTGGAAGATGGGAAGGACTTTGCTGGGGCTTTGGAAGCT
1 GGGCTATGGAAGATGAGAAGGACTTTGCTGGGGATTTAGAAGCT
7128 GG
1 GG
7130 AGAGGTAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 37 0.95
45 2 0.05
ACGTcount: A:0.21, C:0.10, G:0.42, T:0.27
Consensus pattern (44 bp):
GGGCTATGGAAGATGAGAAGGACTTTGCTGGGGATTTAGAAGCT
Found at i:7102 original size:74 final size:74
Alignment explanation
Indices: 6972--7134 Score: 256
Period size: 74 Copynumber: 2.2 Consensus size: 74
6962 CATGAGCATT
6972 TGGAAGCTGAGAGGACGTTGCTGGGGATTTAGAAGCTGGGGCTTTGAAAGATGGGAAGGACTTTG
1 TGGAAGCTGAGAGGACGTTGCTGGGGATTTAGAAGCTGGGGCTTTGAAAGATGGGAAGGACTTTG
7037 ATGGGGCTA
66 ATGGGGCTA
* * *
7046 TGGAAGCTAGAGAGGACTTTGTTGGGGATTTAGAAGCT-GGGCTTTGGAAGATGGGAAGGACTTT
1 TGGAAGCT-GAGAGGACGTTGCTGGGGATTTAGAAGCTGGGGCTTTGAAAGATGGGAAGGACTTT
* *
7110 GCTGGGGCTT
65 GATGGGGCTA
7120 TGGAAGCTGGAGAGG
1 TGGAAGCT-GAGAGG
7135 TAACTATCTC
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 55 0.67
75 27 0.33
ACGTcount: A:0.23, C:0.09, G:0.42, T:0.25
Consensus pattern (74 bp):
TGGAAGCTGAGAGGACGTTGCTGGGGATTTAGAAGCTGGGGCTTTGAAAGATGGGAAGGACTTTG
ATGGGGCTA
Found at i:12325 original size:27 final size:27
Alignment explanation
Indices: 12259--12364 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 27
12249 TGTGAACTTA
* * *
12259 AAATGACCACAATGCCCCTTGAGTGTGC
1 AAATGACCAAAATGCCCCTGGA-TGTAC
*
12287 AAATGACCAAAATGCCCCTGGATGTTC
1 AAATGACCAAAATGCCCCTGGATGTAC
* * * *
12314 AAATGACTAAAATGCCCCTGAATATAA
1 AAATGACCAAAATGCCCCTGGATGTAC
*
12341 AAATGACCAAAATGCCCCTAGATG
1 AAATGACCAAAATGCCCCTGGATG
12365 ACCCTAGTGC
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 46 0.70
28 20 0.30
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATGTAC
Found at i:13175 original size:56 final size:56
Alignment explanation
Indices: 13113--13223 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
13103 TTACTCATGG
*
13113 GCCAATGGGCCACTTAATATTAAATCATTA-TTATAAAAAGTTTGCAAAAACTACTT
1 GCCAATGGGCCACTTAATATTAAACCATTATTTA-AAAAAGTTTGCAAAAACTACTT
13169 GCCAATGGGCCACTTAATATTAAACCATTATTTAAAAAAGTTTGCAAAAACTACT
1 GCCAATGGGCCACTTAATATTAAACCATTATTTAAAAAAGTTTGCAAAAACTACT
13224 CACATGTATC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
56 50 0.94
57 3 0.06
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (56 bp):
GCCAATGGGCCACTTAATATTAAACCATTATTTAAAAAAGTTTGCAAAAACTACTT
Found at i:13550 original size:31 final size:31
Alignment explanation
Indices: 13513--13701 Score: 204
Period size: 31 Copynumber: 6.2 Consensus size: 31
13503 ACGGTGTCCG
* *
13513 ACGTGGCATGCCATGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * *
13544 ATGTGGCACGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* *
13575 ACGTGACACT-CCACATGTACCAAAAAGTGAC
1 ACGTGGCA-TGCCACGTGTACCAAAAAGTGAC
* * *
13606 ACATGGCAAGCCACATGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * * *
13637 ACGTGACACGCCATGTGTACCAAAAAGTAAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* *
13668 ACGTGGCATGCCTCGTGCA-CAAAAAG-GAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
13697 ACGTG
1 ACGTG
13702 CCACGTGTCA
Statistics
Matches: 133, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.05
30 7 0.05
31 119 0.89
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:22860 original size:39 final size:40
Alignment explanation
Indices: 22804--22884 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
22794 TTTAATTCCT
*
22804 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATGAATTAA
* *
22844 ATGTAATA-CTATAATAACTGAAATACTTACATGAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATGAATTAA
22883 AT
1 AT
22885 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.36
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATGAATTAA
Done.