Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2003
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: 169224
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:155775 original size:20 final size:20
Alignment explanation
Indices: 155750--155795 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
155740 GGATACAAGA
*
155750 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
**
155770 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
155790 GAGGGA
1 GAGGGA
155796 GCCTCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.50, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:155945 original size:24 final size:27
Alignment explanation
Indices: 155872--155942 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
155862 AAACAAGCCT
* *
155872 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
155900 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
155927 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
155943 AATGGGTAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:157863 original size:21 final size:22
Alignment explanation
Indices: 157825--157870 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
157815 ATCTGTTGAA
* **
157825 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
157846 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
157868 ACT
1 ACT
157871 TGTCTGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:160337 original size:13 final size:13
Alignment explanation
Indices: 160319--160353 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
160309 AAAGAATTGA
160319 AGAGGGATACAAG
1 AGAGGGATACAAG
160332 AGAGGGATACAAG
1 AGAGGGATACAAG
160345 AGAGGGATA
1 AGAGGGATA
160354 AGGGATACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.06, G:0.40, T:0.09
Consensus pattern (13 bp):
AGAGGGATACAAG
Found at i:160359 original size:20 final size:20
Alignment explanation
Indices: 160334--160371 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
160324 GATACAAGAG
160334 AGGGATACAAGAGAGGGATA
1 AGGGATACAAGAGAGGGATA
**
160354 AGGGATACTTGAGAGGGA
1 AGGGATACAAGAGAGGGA
160372 GGAGGGAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.42, T:0.13
Consensus pattern (20 bp):
AGGGATACAAGAGAGGGATA
Found at i:160377 original size:20 final size:20
Alignment explanation
Indices: 160333--160378 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
160323 GGATACAAGA
*
160333 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
160353 AAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
160373 GAGGGA
1 GAGGGA
160379 GCCTCTATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.48, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:160523 original size:27 final size:27
Alignment explanation
Indices: 160434--160525 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 27
160424 TAGCCATAAA
* * *
160434 TTTTGACAAAT--AAACAAGCCTCCAT
1 TTTTGACAAATACAAAGAAACCACCAT
* *
160459 ATTTGACAAATACAAAGGAAACTACCAT
1 TTTTGACAAATACAAA-GAAACCACCAT
*
160487 TTTTGACAAATACAAA-ATAACCACTAT
1 TTTTGACAAATACAAAGA-AACCACCAT
160514 TTTTGACAAATA
1 TTTTGACAAATA
160526 AATGGATGGC
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
25 10 0.18
26 1 0.02
27 22 0.40
28 22 0.40
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (27 bp):
TTTTGACAAATACAAAGAAACCACCAT
Found at i:162293 original size:28 final size:27
Alignment explanation
Indices: 162238--162308 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
162228 GCCACCCATT
162238 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
*
162265 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
*
162293 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
162309 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:166822 original size:27 final size:27
Alignment explanation
Indices: 166789--166865 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 27
166779 GCCACCCATT
166789 TATTTGTCAAAAATGGTGGTTAT-TTTG
1 TATTTGTCAAAAATGGTGGTT-TCTTTG
* *
166816 TGTTTGTCAAAAATGGTGATTTCCTTTG
1 TATTTGTCAAAAATGGTGGTTT-CTTTG
* *
166844 TATTTGTCAAATATGGAGGTTT
1 TATTTGTCAAAAATGGTGGTTT
166866 GTTTATTGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.02
27 19 0.45
28 22 0.52
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTTCTTTG
Found at i:166844 original size:28 final size:27
Alignment explanation
Indices: 166789--166859 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
166779 GCCACCCATT
*
166789 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGATTATTTTG
*
166816 TGTTTGTCAAAAATGGTGATT-TCCTTTG
1 TATTTGTCAAAAATGGTGATTAT--TTTG
*
166844 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
166860 AGGTTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.50
28 18 0.47
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGATTATTTTG
Found at i:167719 original size:17 final size:17
Alignment explanation
Indices: 167697--167749 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
167687 AACATTTGTG
167697 ATTTTTATTAATATATT
1 ATTTTTATTAATATATT
*
167714 ATTTTTATT--TA-A-G
1 ATTTTTATTAATATATT
*
167727 ATTTTTATTAATATTTT
1 ATTTTTATTAATATATT
167744 ATTTTT
1 ATTTTT
167750 TATTTATAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
13 9 0.31
14 1 0.03
15 4 0.14
17 15 0.52
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
ATTTTTATTAATATATT
Found at i:167730 original size:30 final size:31
Alignment explanation
Indices: 167696--167755 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
167686 TAACATTTGT
167696 GATTTTTATTAATATATTA-TTTTTATTTAA
1 GATTTTTATTAATATATTATTTTTTATTTAA
*
167726 GATTTTTATTAATATTTTATTTTTTATTTA
1 GATTTTTATTAATATATTATTTTTTATTTA
167756 TAACTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (31 bp):
GATTTTTATTAATATATTATTTTTTATTTAA
Found at i:169013 original size:16 final size:18
Alignment explanation
Indices: 168982--169015 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
168972 AGATAATTTT
168982 TAAAATAAATTATAAATA
1 TAAAATAAATTATAAATA
169000 TAAAAT-AA-TATAAATA
1 TAAAATAAATTATAAATA
169016 AAATACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAATAAATTATAAATA
Found at i:169143 original size:16 final size:16
Alignment explanation
Indices: 169112--169145 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
169102 ATTTCACATT
*
169112 AAAAAATAAAAGTAAC
1 AAAAAATAAAACTAAC
*
169128 AAAAAATAAACCTAAC
1 AAAAAATAAAACTAAC
169144 AA
1 AA
169146 CTCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.12, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAAATAAAACTAAC
Done.