Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017589.1 Corchorus olitorius cultivar O-4 contig17622, 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: 25413
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Found at i:15216 original size:12 final size:12
Alignment explanation
Indices: 15199--15223 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15189 TGTTGTCGCC
15199 GGCGTCGGGATT
1 GGCGTCGGGATT
15211 GGCGTCGGGATT
1 GGCGTCGGGATT
15223 G
1 G
15224 ACCATTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.52, T:0.24
Consensus pattern (12 bp):
GGCGTCGGGATT
Found at i:17449 original size:4 final size:4
Alignment explanation
Indices: 17440--17536 Score: 70
Period size: 4 Copynumber: 24.5 Consensus size: 4
17430 GAACACCATT
* * * * * * * *
17440 TCTC TCTC TCTC TCTC TGTC TATC TGTC TGTC TGTC TGTC TGTC TGTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
* * * * *
17488 TGTC TGTC TGTC TATC TGTC TCTC TCTC TCTC TCTC TC-C TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
17535 TC
1 TC
17537 CCTTTGTTTA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
3 3 0.03
4 83 0.97
ACGTcount: A:0.02, C:0.37, G:0.11, T:0.49
Consensus pattern (4 bp):
TCTC
Found at i:17453 original size:8 final size:8
Alignment explanation
Indices: 17442--17535 Score: 91
Period size: 8 Copynumber: 11.9 Consensus size: 8
17432 ACACCATTTC
*
17442 TCTCTCTC
1 TCTCTCTG
17450 TCTCTCTG
1 TCTCTCTG
*
17458 TCTATCTG
1 TCTCTCTG
*
17466 TCTGTCTG
1 TCTCTCTG
*
17474 TCTGTCTG
1 TCTCTCTG
*
17482 TCTGTCTG
1 TCTCTCTG
*
17490 TCTGTCTG
1 TCTCTCTG
*
17498 TCTATCTG
1 TCTCTCTG
*
17506 TCTCTCTC
1 TCTCTCTG
*
17514 TCTCTCTC
1 TCTCTCTG
*
17522 TCTC-CTC
1 TCTCTCTG
17529 TCTCTCT
1 TCTCTCT
17536 CCCTTTGTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
7 7 0.09
8 72 0.91
ACGTcount: A:0.02, C:0.36, G:0.12, T:0.50
Consensus pattern (8 bp):
TCTCTCTG
Found at i:17469 original size:12 final size:12
Alignment explanation
Indices: 17454--17508 Score: 92
Period size: 12 Copynumber: 4.6 Consensus size: 12
17444 TCTCTCTCTC
*
17454 TCTGTCTATCTG
1 TCTGTCTGTCTG
17466 TCTGTCTGTCTG
1 TCTGTCTGTCTG
17478 TCTGTCTGTCTG
1 TCTGTCTGTCTG
*
17490 TCTGTCTGTCTA
1 TCTGTCTGTCTG
17502 TCTGTCT
1 TCTGTCT
17509 CTCTCTCTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.04, C:0.25, G:0.20, T:0.51
Consensus pattern (12 bp):
TCTGTCTGTCTG
Found at i:17521 original size:12 final size:12
Alignment explanation
Indices: 17440--17536 Score: 88
Period size: 12 Copynumber: 8.2 Consensus size: 12
17430 GAACACCATT
*
17440 TCTCTCTCTCTC
1 TCTCTGTCTCTC
*
17452 TCTCTGTCTATC
1 TCTCTGTCTCTC
* *
17464 TGTCTGTCTGTC
1 TCTCTGTCTCTC
* *
17476 TGTCTGTCTGTC
1 TCTCTGTCTCTC
* *
17488 TGTCTGTCTGTC
1 TCTCTGTCTCTC
*
17500 TATCTGTCTCTC
1 TCTCTGTCTCTC
*
17512 TCTCTCTCTCTC
1 TCTCTGTCTCTC
*
17524 TC-CTCTCTCTC
1 TCTCTGTCTCTC
17535 TC
1 TC
17537 CCTTTGTTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
11 11 0.14
12 66 0.86
ACGTcount: A:0.02, C:0.37, G:0.11, T:0.49
Consensus pattern (12 bp):
TCTCTGTCTCTC
Found at i:17759 original size:3 final size:3
Alignment explanation
Indices: 17740--17809 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
17730 AATAATAATA
* *
17740 ATT ATT TTT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17788 ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
17810 AGTCAGTAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:25236 original size:2 final size:2
Alignment explanation
Indices: 25229--25264 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25219 AACCAAAGTG
25229 AT AT AT AT AT 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 AT AT AT AT AT
25265 CAATACAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.