Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold464
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: 23411
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:280 original size:30 final size:30
Alignment explanation
Indices: 246--331 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 30
236 GCTCACTCCT
246 AGCTCATA-TTTAGCTCACGAGCTAAACCTC
1 AGCTCA-ACTTTAGCTCACGAGCTAAACCTC
* * * * * *
276 AGCTCAACTTCAGCTTAGGAGTTTAGCCTC
1 AGCTCAACTTTAGCTCACGAGCTAAACCTC
306 AGCTCAACTTTAGCTCACGAGCTAAA
1 AGCTCAACTTTAGCTCACGAGCTAAA
332 GCGTAGCTCA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (30 bp):
AGCTCAACTTTAGCTCACGAGCTAAACCTC
Found at i:340 original size:30 final size:31
Alignment explanation
Indices: 246--341 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
236 GCTCACTCCT
246 AGCTCATA-TTTAGCTCACGAGCTAAA-CCTC
1 AGCTCA-ACTTTAGCTCACGAGCTAAAGCCTC
* * * **
276 AGCTCAACTTCAGCTTAGGAG-TTTAGCCTC
1 AGCTCAACTTTAGCTCACGAGCTAAAGCCTC
*
306 AGCTCAACTTTAGCTCACGAGCTAAAGCGT-
1 AGCTCAACTTTAGCTCACGAGCTAAAGCCTC
336 AGCTCA
1 AGCTCA
342 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 3 0.06
30 44 0.85
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (31 bp):
AGCTCAACTTTAGCTCACGAGCTAAAGCCTC
Found at i:1931 original size:24 final size:24
Alignment explanation
Indices: 1904--1954 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1894 GCCTAGCCTC
1904 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAAC-GGGGCAAAGCCCT
**
1928 TTTTGGTAAACGGGGCAAAGCCCT
1 TTTTAATAAACGGGGCAAAGCCCT
1952 TTT
1 TTT
1955 CGCACTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (24 bp):
TTTTAATAAACGGGGCAAAGCCCT
Found at i:2029 original size:21 final size:21
Alignment explanation
Indices: 2002--2062 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1992 TATAGTGAGT
2002 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
* **
2023 ATCTCATAAAATATCATGTGC
1 ATATCATAGCATATCATGTGC
*
2044 ATATTAT-GTCATATCATGT
1 ATATCATAG-CATATCATGT
2063 ATAACAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.38
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:14692 original size:32 final size:33
Alignment explanation
Indices: 14629--14693 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
14619 ACTCTCCTTA
*
14629 ATTCGTTCACACCTATGTTCACATGGCAAGACC
1 ATTCGTTCACACCTATGTTCACATAGCAAGACC
14662 ATTCGGTTCACA-CT-TGTTCACACTAG-AAGACC
1 ATTC-GTTCACACCTATGTTCACA-TAGCAAGACC
14694 TTCAAACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 14 0.48
33 8 0.28
34 7 0.24
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (33 bp):
ATTCGTTCACACCTATGTTCACATAGCAAGACC
Found at i:16089 original size:34 final size:34
Alignment explanation
Indices: 16051--16118 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
16041 AAATTTGATA
*
16051 GACAACA-ACACAGGGGGGAATATGAAACAATTGT
1 GACAACAGACACA-GGGGAAATATGAAACAATTGT
*
16085 GACAACAGCCACAGGGGAAATATGAAACAATTGT
1 GACAACAGACACAGGGGAAATATGAAACAATTGT
16119 AAGTTAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.15
Consensus pattern (34 bp):
GACAACAGACACAGGGGAAATATGAAACAATTGT
Found at i:18863 original size:22 final size:22
Alignment explanation
Indices: 18820--18883 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
18810 AACACTAGAT
18820 TACCATATTCGTACCAAA-TCCA
1 TACCAT-TTCGTACCAAATTCCA
*
18842 TACCATTTCATACCAAATTCCA
1 TACCATTTCGTACCAAATTCCA
18864 TACCATTTCGTACC-AATTCC
1 TACCATTTCGTACCAAATTCC
18884 CAAAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 16 0.41
22 23 0.59
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (22 bp):
TACCATTTCGTACCAAATTCCA
Found at i:21049 original size:11 final size:11
Alignment explanation
Indices: 21033--21072 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
21023 GTTGTAAAGT
21033 TTTTATTTTTA
1 TTTTATTTTTA
21044 TTTTATTTTTA
1 TTTTATTTTTA
* *
21055 TTTCA-TATTA
1 TTTTATTTTTA
21065 TTTTATTT
1 TTTTATTT
21073 ACTTAGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATTTTTA
Done.