Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3755
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: 31084
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Found at i:5080 original size:40 final size:40
Alignment explanation
Indices: 5050--5259 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
5040 GGACTAAGAT
* * * *
5050 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
5090 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
5130 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* *
5170 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * *
5210 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
5249 CCGAAGGCATT
1 CCGAAGGCATT
5260 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 34 0.21
40 125 0.79
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:5096 original size:80 final size:80
Alignment explanation
Indices: 4997--5259 Score: 273
Period size: 80 Copynumber: 3.3 Consensus size: 80
4987 TTGAATGCTG
* * * *
4997 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-AAGTGAATAAATCCGGACTAAG-TCCCGAAGGCAT
*
5060 TTGTGCGAGATACTAAA
64 TCGTGCGAGATACTAAA
* * * **
5077 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTGAATAAATCCGGACTAAGTCCCGAAGGCATTC
* *
5142 GTGCGAGTTATTAAA
66 GTGCGAGATACTAAA
* * ** *
5157 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTG-TTAAATCCGGGTTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAG-TGAATAAATCCGGACTAAGTCCCGAAGGCATT
* *
5221 -GTGTGAGTTACTAAA
65 CGTGCGAGATACTAAA
* * *
5236 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
5260 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
79 35 0.22
80 119 0.74
81 7 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTGAATAAATCCGGACTAAGTCCCGAAGGCATTC
GTGCGAGATACTAAA
Found at i:5211 original size:120 final size:120
Alignment explanation
Indices: 4997--5259 Score: 325
Period size: 120 Copynumber: 2.2 Consensus size: 120
4987 TTGAATGCTG
* * *
4997 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
5061 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * * **
5117 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * *
5180 TCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
5236 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
5260 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
119 35 0.29
120 81 0.66
121 6 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:5279 original size:79 final size:80
Alignment explanation
Indices: 5050--5294 Score: 253
Period size: 80 Copynumber: 3.1 Consensus size: 80
5040 GGACTAAGAT
* * * * * ** * *
5050 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TT
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAG-GAGCT
5114 AAATCCGGGTTAAGTC
65 AAATCCGGGTTAAGTC
* * * ** ** *
5130 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
5195 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
5210 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
5274 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
5288 CCGAAGG
1 CCGAAGG
5295 TACGTGATTT
Statistics
Matches: 144, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
78 14 0.10
79 47 0.33
80 83 0.58
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:13151 original size:40 final size:40
Alignment explanation
Indices: 13096--13257 Score: 265
Period size: 40 Copynumber: 4.0 Consensus size: 40
13086 CGATTGATAC
13096 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
13136 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
*
13176 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
13216 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
13256 CC
1 CC
13258 AGCTAAACTC
Statistics
Matches: 116, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
39 3 0.03
40 112 0.97
41 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:30721 original size:80 final size:79
Alignment explanation
Indices: 30628--30811 Score: 327
Period size: 80 Copynumber: 2.3 Consensus size: 79
30618 GTAACTCAAC
30628 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG-ATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAA-CCGGAT
30692 TTAACAAACTCGCACG
65 TTAAC-AACTCGCACG
*
30708 ATTGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCGGATT
30773 TAACAACTCGCACG
66 TAACAACTCGCACG
30787 AATGCCTTCGGGACTTAA-CCGGATT
1 AATGCCTTCGGGACTTAACCCGGATT
30812 AGTATCTCGC
Statistics
Matches: 101, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
78 7 0.07
79 27 0.27
80 50 0.50
81 17 0.17
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCGGATT
TAACAACTCGCACG
Found at i:30742 original size:40 final size:40
Alignment explanation
Indices: 30628--30811 Score: 329
Period size: 39 Copynumber: 4.7 Consensus size: 40
30618 GTAACTCAAC
30628 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
30668 -ATGCCTTCGGGACTTAACCCGGATTTAACAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAC-AACTCGCACG
*
30708 ATTGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
30748 AATGCCTTCGGGACTTAA-CCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
30787 AATGCCTTCGGGACTTAA-CCGGATT
1 AATGCCTTCGGGACTTAACCCGGATT
30812 AGTATCTCGC
Statistics
Matches: 140, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
39 75 0.54
40 37 0.26
41 28 0.20
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Done.