Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_662 ID=scaffold_662-JGI_221_v2.0
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: 4826
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Found at i:341 original size:43 final size:43
Alignment explanation
Indices: 291--605 Score: 350
Period size: 43 Copynumber: 7.4 Consensus size: 43
281 CGTTTTTACC
* * *
291 CACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTCC
1 CACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCT
* * * * *
334 CACAAACGCCGCTATAGACCACGACCTTTAACGGCACTTTTGT
1 CACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCT
* * *
377 CAC-AACGCCGTTAAAGACCATGACCTTTAGCTGCGCTTTTAT
1 CACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCT
* *
419 CACAAACGCCGCTAAAG-CTCATGACCTTTAGCTGCGCTTTTGT
1 CACAAACGCCGCTAAAGAC-CATGACCTTTAGCGGCGCTTTTCT
* * *
462 AACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTAT
1 CACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCT
* *
505 CACAAACGCCACTAAAG-CTCATGACCTTTAGCGGCGCTTTTGT
1 CACAAACGCCGCTAAAGAC-CATGACCTTTAGCGGCGCTTTTCT
* * * * * * *
548 TACAAACGCCGCTATAGAACA-AACCTTTAGCGACGCTTCTCG
1 CACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCT
*
590 CAAAAACGCCGCTAAA
1 CACAAACGCCGCTAAA
606 AACATATCAT
Statistics
Matches: 231, Mismatches: 36, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
42 66 0.29
43 164 0.71
44 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
CACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCT
Found at i:500 original size:86 final size:86
Alignment explanation
Indices: 292--605 Score: 393
Period size: 85 Copynumber: 3.7 Consensus size: 86
282 GTTTTTACCC
* * * ** * *
292 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTCCCACAAACGCCGCTATAGAC-CAC
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAG-CTCAT
* * *
356 GACCTTTAACGGCACTTTTGTC
65 GACCTTTAGCGGCGCTTTTGTA
*
378 AC-AACGCCGTTAAAGACCATGACCTTTAGCTG-CGCTTTTATCACAAACGCCGCTAAAGCTCAT
1 ACAAACGCCGCTAAAGACCATGACCTTTAGC-GACGCTTTTATCACAAACGCCGCTAAAGCTCAT
*
441 GACCTTTAGCTGCGCTTTTGTA
65 GACCTTTAGCGGCGCTTTTGTA
*
463 ACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAACGCCACTAAAGCTCATG
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAGCTCATG
*
528 ACCTTTAGCGGCGCTTTTGTT
66 ACCTTTAGCGGCGCTTTTGTA
* * * * ** *
549 ACAAACGCCGCTATAGAACA-AACCTTTAGCGACGCTTCTCGCAAAAACGCCGCTAAA
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAA
606 AACATATCAT
Statistics
Matches: 201, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.00
85 102 0.51
86 98 0.49
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (86 bp):
ACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAGCTCATG
ACCTTTAGCGGCGCTTTTGTA
Found at i:577 original size:171 final size:171
Alignment explanation
Indices: 292--605 Score: 409
Period size: 171 Copynumber: 1.8 Consensus size: 171
282 GTTTTTACCC
* * * * *
292 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTCCCACAAACGCCGCTATAGACCACG
1 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGCTTTTACCACAAACGCCACTAAAGACCACG
* * * * *
357 ACCTTTAACGGCACTTTTGTCACAACGCCGTTAAAGACCATGACCTTTAGCTG-CGCTTTTATCA
66 ACCTTTAACGGCACTTTTGTCACAACGCCGCTAAAGAACATAACCTTTAGC-GACGCTTCTAGCA
*
421 CAAACGCCGCTAAAGCTCATGACCTTTAGCTGCGCTTTTGTA
130 AAAACGCCGCTAAAGCTCATGACCTTTAGCTGCGCTTTTGTA
* * *
463 ACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAACGCCACTAAAG-CTCAT
1 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGCTTTTACCACAAACGCCACTAAAGAC-CAC
* * * * *
527 GACCTTTAGCGGCGCTTTTGTTACAAACGCCGCTATAGAACA-AACCTTTAGCGACGCTTCTCGC
65 GACCTTTAACGGCACTTTTGTCAC-AACGCCGCTAAAGAACATAACCTTTAGCGACGCTTCTAGC
591 AAAAACGCCGCTAAA
129 AAAAACGCCGCTAAA
606 AACATATCAT
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
170 2 0.02
171 105 0.87
172 14 0.12
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (171 bp):
ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGCTTTTACCACAAACGCCACTAAAGACCACG
ACCTTTAACGGCACTTTTGTCACAACGCCGCTAAAGAACATAACCTTTAGCGACGCTTCTAGCAA
AAACGCCGCTAAAGCTCATGACCTTTAGCTGCGCTTTTGTA
Found at i:4381 original size:19 final size:19
Alignment explanation
Indices: 4359--4404 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
4349 AAAATTATAT
4359 TTTTTATTTTT-TATTTCA
1 TTTTTATTTTTGTATTTCA
*
4377 TTTTTATTTTTGTATTTTA
1 TTTTTATTTTTGTATTTCA
*
4396 ATTTTATTT
1 TTTTTATTT
4405 CTTATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTATTTTTGTATTTCA
Found at i:4399 original size:25 final size:26
Alignment explanation
Indices: 4356--4409 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
4346 GATAAAATTA
*
4356 TATTTTTTATTTTTTATTTCATTT-T
1 TATTTTTTATTTTTAATTTCATTTCT
*
4381 TATTTTTGTA-TTTTAATTTTATTTCT
1 TATTTTT-TATTTTTAATTTCATTTCT
4407 TAT
1 TAT
4410 AATTTGGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.76
Consensus pattern (26 bp):
TATTTTTTATTTTTAATTTCATTTCT
Done.