Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3529
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: 14539
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Found at i:695 original size:40 final size:40
Alignment explanation
Indices: 633--774 Score: 166
Period size: 40 Copynumber: 3.6 Consensus size: 40
623 CTCGCACAAG
* * * * *
633 GCCTTCGGGTC-TAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
672 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGC-CAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
711 GCCTTC--GACCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
751 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
775 CATTCGAGTA
Statistics
Matches: 87, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
37 2 0.02
38 18 0.21
39 24 0.28
40 29 0.33
41 12 0.14
42 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:3888 original size:40 final size:40
Alignment explanation
Indices: 3837--4218 Score: 628
Period size: 40 Copynumber: 9.6 Consensus size: 40
3827 CATTTGAATG
3837 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
3877 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
3917 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
3957 ATATCCGGGC-AAGACCCGAAGGCATTTGTGCG-ATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
3995 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
4035 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAA-TGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
4074 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
4114 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
4154 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
4194 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
4219 ATTGAGCTTG
Statistics
Matches: 322, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
38 15 0.05
39 81 0.25
40 225 0.70
41 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:4222 original size:80 final size:80
Alignment explanation
Indices: 3837--4218 Score: 628
Period size: 79 Copynumber: 4.8 Consensus size: 80
3827 CATTTGAATG
3837 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCA
3902 TTTGTGCGAATTGAT
66 TTTGTGCGAATTGAT
*
3917 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGATATATCCGGGC-AAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCA
3981 TTTGTGCG-ATTGAT
66 TTTGTGCGAATTGAT
* *
3995 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGATAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCA
4060 TTTGTGCGAA-TGAT
66 TTTGTGCGAATTGAT
* *
4074 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCA
*
4139 ATTGTGC-AAGTTGAT
66 TTTGTGCGAA-TTGAT
* * * * *
4154 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCA
4219 ATTGAGCTTG
Statistics
Matches: 282, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
78 55 0.20
79 115 0.41
80 112 0.40
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAATTGAT
Found at i:6028 original size:38 final size:38
Alignment explanation
Indices: 5986--6061 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
5976 CAAGAACTCC
5986 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
6024 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
6062 AAAGGATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:12721 original size:39 final size:40
Alignment explanation
Indices: 12676--12843 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
12666 CGGGGTTTAG
* * *
12676 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
12715 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
12755 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
12795 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
12836 CCGGATAT
1 CCGGATAT
12844 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:12826 original size:41 final size:40
Alignment explanation
Indices: 12699--12843 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
12689 CTCGCACAAG
* * * * *
12699 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
12739 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
12779 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
12820 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
12844 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Done.