Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2239
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, 613
Length: 1023
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Found at i:144 original size:17 final size:17
Alignment explanation
Indices: 132--276 Score: 134
Period size: 17 Copynumber: 8.4 Consensus size: 17
122 AAAAAAAATG
132 TCGTGTTTTAAAAATTT
1 TCGTGTTTTAAAAATTT
149 TCGTGTTTCT-AAAATTT
1 TCGTGTTT-TAAAAATTT
* * *
166 CCCTGTTTTAAAAATTC
1 TCGTGTTTTAAAAATTT
* * *
183 CCGTGTTTTTAAAAAAATG
1 TCGTG-TTTT-AAAAATTT
*
202 TCGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTT
219 TCGTGTTTCT-AAAATTT
1 TCGTGTTT-TAAAAATTT
* *
236 TCGTG-TTTACAAATTC
1 TCGTGTTTTAAAAATTT
*
252 TCGTGTTTTCAAAAATTC
1 TCGTGTTTT-AAAAATTT
270 TCGTGTT
1 TCGTGTT
277 AAAAAAAAAC
Statistics
Matches: 106, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
15 1 0.01
16 13 0.12
17 60 0.57
18 22 0.21
19 10 0.09
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (17 bp):
TCGTGTTTTAAAAATTT
Found at i:227 original size:70 final size:69
Alignment explanation
Indices: 114--266 Score: 225
Period size: 70 Copynumber: 2.2 Consensus size: 69
104 TTTTTTAAAT
* *
114 CGTGTTTCAAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAA
1 CGTGTTTTAAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATTTCCCTG-TTTAAAA
179 ATTCC
65 ATTCC
* * * *
184 CGTGTTTTTAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATTTTCGTGTTTACAAA
1 CGTGTTTTAAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAAAA
*
249 TTCT
66 TTCC
*
253 CGTGTTTTCAAAAA
1 CGTGTTTTAAAAAA
267 TTCTCGTGTT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 23 0.31
70 52 0.69
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (69 bp):
CGTGTTTTAAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAAAA
TTCC
Found at i:282 original size:16 final size:17
Alignment explanation
Indices: 113--276 Score: 125
Period size: 17 Copynumber: 9.4 Consensus size: 17
103 ATTTTTTAAA
* *
113 TCGTGTTTCAAAAAAAATG
1 TCGTGTTTC--AAAAATTC
* *
132 TCGTGTTTTAAAAATTT
1 TCGTGTTTCAAAAATTC
*
149 TCGTGTTTCTAAAATT-
1 TCGTGTTTCAAAAATTC
* *
165 TCCCTGTTTTAAAAATTC
1 T-CGTGTTTCAAAAATTC
* * * *
183 CCGTGTTTTTAAAAAAATG
1 TCGTG--TTTCAAAAATTC
*
202 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTC
* *
219 TCGTGTTTCTAAAATTT
1 TCGTGTTTCAAAAATTC
*
236 TCGTGTTT-ACAAATTC
1 TCGTGTTTCAAAAATTC
252 TCGTGTTTTCAAAAATTC
1 TCGTG-TTTCAAAAATTC
270 TCGTGTT
1 TCGTGTT
277 AAAAAAAAAC
Statistics
Matches: 117, Mismatches: 22, Indels: 14
0.76 0.14 0.09
Matches are distributed among these distances:
16 11 0.09
17 73 0.62
18 12 0.10
19 21 0.18
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTC
Found at i:283 original size:18 final size:18
Alignment explanation
Indices: 246--284 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
236 TCGTGTTTAC
***
246 AAATTCTCGTGTTTTCAA
1 AAATTCTCGTGTTAAAAA
264 AAATTCTCGTGTTAAAAA
1 AAATTCTCGTGTTAAAAA
282 AAA
1 AAA
285 ACTTTCGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (18 bp):
AAATTCTCGTGTTAAAAA
Done.