Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1380
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: 1881
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Found at i:57 original size:15 final size:15
Alignment explanation
Indices: 7--90 Score: 80
Period size: 16 Copynumber: 5.5 Consensus size: 15
1 CTAAAC
*
7 CCCTAAACCCCTAAAA
1 CCCTAAAACCC-AAAA
23 CCCTAAAACCCTAAAA
1 CCCTAAAACCC-AAAA
**
39 CCCTAAAACCCCGAA
1 CCCTAAAACCCAAAA
* *
54 CCCTACAACCCTAAA
1 CCCTAAAACCCAAAA
*
69 CCCT-AAACCCTACAA
1 CCCTAAAACCC-AAAA
84 CCCTAAA
1 CCCTAAA
91 CCCTGAACAC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
14 5 0.09
15 24 0.42
16 28 0.49
ACGTcount: A:0.43, C:0.44, G:0.01, T:0.12
Consensus pattern (15 bp):
CCCTAAAACCCAAAA
Found at i:70 original size:7 final size:7
Alignment explanation
Indices: 1--312 Score: 166
Period size: 7 Copynumber: 42.1 Consensus size: 7
1 CTAAACCC
1 CTAAA-CC
9 CTAAACCC
1 CTAAA-CC
17 CTAAAACC
1 CT-AAACC
25 CTAAAACC
1 CT-AAACC
33 CTAAAACC
1 CT-AAACC
41 CTAAAACC
1 CT-AAACC
**
49 CCGAACC
1 CTAAACC
56 CTACAACC
1 CTA-AACC
64 CTAAACC
1 CTAAACC
71 CTAAACC
1 CTAAACC
78 CTACAACC
1 CTA-AACC
86 CTAAACC
1 CTAAACC
*
93 CTGAACAC
1 CTAAAC-C
101 C-AAACC
1 CTAAACC
*
107 CTAAACT
1 CTAAACC
*
114 GTAAACC
1 CTAAACC
*
121 ATAAAACC
1 CT-AAACC
*
129 ATAAAACC
1 CT-AAACC
*
137 ATAAACC
1 CTAAACC
*
144 CCAAACC
1 CTAAACC
*
151 CCAAACC
1 CTAAACC
*
158 CTAAGCC
1 CTAAACC
*
165 CTAAGCC
1 CTAAACC
*
172 CTAAGCC
1 CTAAACC
179 CTAAAACC
1 CT-AAACC
*
187 CCAAACC
1 CTAAACC
*
194 CTAGACC
1 CTAAACC
* *
201 CCAGACC
1 CTAAACC
* **
208 CCAGGTCC
1 CTA-AACC
216 C-AAACAC
1 CTAAAC-C
223 C-AAACAC
1 CTAAAC-C
230 C-AAACAC
1 CTAAAC-C
237 C-AAACCC
1 CTAAA-CC
*
244 CTAAGCC
1 CTAAACC
251 CTAAACC
1 CTAAACC
258 CTAAAAACC
1 CT--AAACC
*
267 CTACACC
1 CTAAACC
274 CTAAAAACC
1 CT--AAACC
283 CTAAACC
1 CTAAACC
*
290 CCAAACCC
1 CTAAA-CC
**
298 CTAAATA
1 CTAAACC
305 CTAAACC
1 CTAAACC
312 C
1 C
313 AAGCCAGGAT
Statistics
Matches: 256, Mismatches: 32, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
6 3 0.01
7 151 0.59
8 86 0.34
9 16 0.06
ACGTcount: A:0.43, C:0.43, G:0.04, T:0.11
Consensus pattern (7 bp):
CTAAACC
Found at i:274 original size:16 final size:16
Alignment explanation
Indices: 249--290 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
239 AACCCCTAAG
249 CCCTAAACCCTAAAAA
1 CCCTAAACCCTAAAAA
*
265 CCCTACACCCTAAAAA
1 CCCTAAACCCTAAAAA
281 CCCTAAACCC
1 CCCTAAACCC
291 CAAACCCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.45, G:0.00, T:0.12
Consensus pattern (16 bp):
CCCTAAACCCTAAAAA
Found at i:371 original size:32 final size:32
Alignment explanation
Indices: 330--399 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
320 GATATGCAAA
* *
330 GAATAGAATAAATCC-AAACCGGGATATGCTTG
1 GAATAGAATAAA-CCTAAACCGGGATATCCGTG
* *
362 GAATGGAATAAACCTAAGCCGGGATATCCGTG
1 GAATAGAATAAACCTAAACCGGGATATCCGTG
394 GAATAG
1 GAATAG
400 GATATCCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.20
Consensus pattern (32 bp):
GAATAGAATAAACCTAAACCGGGATATCCGTG
Done.