Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015814.1 Corchorus olitorius cultivar O-4 contig15847, 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: 6713
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Found at i:1983 original size:2 final size:2
Alignment explanation
Indices: 1976--2001 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1966 ATTTAAAAAC
1976 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2002 TAAGTCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2015 original size:51 final size:51
Alignment explanation
Indices: 1922--2049 Score: 217
Period size: 51 Copynumber: 2.6 Consensus size: 51
1912 ATTTGAGTAA
* *
1922 AAAAAAATACATATATATATA-ATA-AT-TATTAAGTCCAATTAACCATTT
1 AAAAACATATATATATATATATATATATATATTAAGTCCAATTAACCATTT
1970 AAAAACATATATATATATATATATATATATATTAAGTCCAATTAACCATTT
1 AAAAACATATATATATATATATATATATATATTAAGTCCAATTAACCATTT
2021 AAAAACATATATATATATATATATATATA
1 AAAAACATATATATATATATATATATATA
2050 GATGAGTTAA
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
48 19 0.25
49 3 0.04
50 2 0.03
51 51 0.68
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (51 bp):
AAAAACATATATATATATATATATATATATATTAAGTCCAATTAACCATTT
Found at i:4106 original size:2 final size:2
Alignment explanation
Indices: 4099--4135 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4089 CACCAAGAAA
4099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4136 CTAAATAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4888 original size:15 final size:14
Alignment explanation
Indices: 4848--4899 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
4838 TGTCAAAATA
* * *
4848 TATATATATATATA
1 TATATGTATGTATG
*
4862 TATATGTGTGTATG
1 TATATGTATGTATG
4876 TATTATGTATGTATG
1 TA-TATGTATGTATG
4891 TATATGTAT
1 TATATGTAT
4900 TATTAAAGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (14 bp):
TATATGTATGTATG
Found at i:5097 original size:31 final size:31
Alignment explanation
Indices: 5059--5120 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5049 AAGTTTTGTA
5059 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
*
5090 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
5121 TTTCGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCACCTATTATACCCTTATT
Found at i:5351 original size:22 final size:21
Alignment explanation
Indices: 5309--5351 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
5299 ATATCCTTAA
* *
5309 AACTATTTATTTTTACCATTT
1 AACTATTTACTTTTACAATTT
*
5330 AACTATTTTACTTTTATAATTT
1 AACTA-TTTACTTTTACAATTT
5352 TAATCAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (21 bp):
AACTATTTACTTTTACAATTT
Found at i:5370 original size:92 final size:93
Alignment explanation
Indices: 5156--5416 Score: 443
Period size: 92 Copynumber: 2.8 Consensus size: 93
5146 TTGTTTAAAT
* *
5156 TTTTATAGTTTTAGTCAACTAAAATCTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
5221 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATTTAACTATTTTAC
* * *
5249 TTTTATAGTTTTACTCAACTAAAACCTCTATTTTTATTTAATTAAATCTAATATCCTTAAAACTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
5314 -TTTATTTTTACCATTTAACTATTTTAC
66 TTTTATTTTTACCATTTAACTATTTTAC
* *
5341 TTTTATAATTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATCTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
5406 TTTTATTTTTA
66 TTTTATTTTTA
5417 TGATATTACT
Statistics
Matches: 158, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
92 86 0.54
93 72 0.46
ACGTcount: A:0.33, C:0.13, G:0.01, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTAACTATTTTAC
Done.