Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2766
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: 70646
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1980 original size:40 final size:39
Alignment explanation
Indices: 1821--2039 Score: 282
Period size: 38 Copynumber: 5.6 Consensus size: 39
1811 TCCTCGTTCA
* * * * *
1821 AATGCCTTCGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACG
* *
1859 AATGCCTTCGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACG
1898 -ATGCCTTCGGACTTAACCCGGATTTAA-AACTCGCACG
1 AATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACG
1935 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACG
* * *
1975 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACG
* *
2015 AAGGCCTTCGGATCTTAATCCGGAT
1 AATGCCTTCGGA-CTTAACCCGGAT
2040 ATATTCACTT
Statistics
Matches: 165, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
37 10 0.06
38 67 0.41
39 22 0.13
40 66 0.40
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:2062 original size:80 final size:79
Alignment explanation
Indices: 1862--2078 Score: 228
Period size: 80 Copynumber: 2.8 Consensus size: 79
1852 CTCACACAAT
* * * * *
1862 GCCTTC-GGACATAACCCGGATTTAACAACTCGCACG-ATGCCTTC-GGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATATAATAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTA
* *
1924 AAACTCGCACGAAT
66 AAACTCGCACAAAG
* * *
1938 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATATAATAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTA
* *
2003 GTATCTCGCACAAAG
66 -AAACTCGCACAAAG
* * * *
2018 GCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGA-CTTAACCCGGATATAATAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
2079 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
76 6 0.05
77 28 0.23
78 8 0.07
79 21 0.17
80 54 0.44
81 5 0.04
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (79 bp):
GCCTTCGGGACTTAACCCGGATATAATAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTA
AAACTCGCACAAAG
Found at i:2078 original size:40 final size:39
Alignment explanation
Indices: 1856--2078 Score: 199
Period size: 40 Copynumber: 5.7 Consensus size: 39
1846 TAGTAACTCA
* * *
1856 CACAATGCCTTC-GGACATAACCCGGATTTAACAAC-TCG
1 CACAAAGCCTTCGGGACTTAACCCGGATTTAA-TACTTCG
* * *
1894 CACGATGCCTTC-GGACTTAACCCGGATTTAAAAC-TCG
1 CACAAAGCCTTCGGGACTTAACCCGGATTTAATACTTCG
*
1931 CACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCG
1 CAC-AAAGCCTTCGGGACTTAACCCGGATTTAAT-ACTTCG
* *
1971 CACGAATGCCTTCGGGACTTAACCCGGATTTAGTA-TCTCG
1 CAC-AAAGCCTTCGGGACTTAACCCGGATTTAATACT-TCG
* * * *
2011 CACAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAG
1 CACAAA-GCCTTCGGGA-CTTAACCCGGATTTAAT-ACTTCG
*
2052 CACAAAGCCTTCGGGACTTAGCCCGGA
1 CACAAAGCCTTCGGGACTTAACCCGGA
2079 CAGCATTCAA
Statistics
Matches: 163, Mismatches: 12, Indels: 18
0.84 0.06 0.09
Matches are distributed among these distances:
37 9 0.06
38 37 0.23
39 25 0.15
40 79 0.48
41 12 0.07
42 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (39 bp):
CACAAAGCCTTCGGGACTTAACCCGGATTTAATACTTCG
Found at i:9817 original size:40 final size:40
Alignment explanation
Indices: 9719--9981 Score: 291
Period size: 40 Copynumber: 6.6 Consensus size: 40
9709 TCCTCGTTCA
* * * ** *
9719 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
9758 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
9798 ACTGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
9838 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
9878 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
9918 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
9958 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
9982 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
39 37 0.19
40 152 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:38638 original size:42 final size:42
Alignment explanation
Indices: 38579--38667 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
38569 GAAAAAAGTC
38579 AAAATTTAAATGGCCCAAAGGTGAGTGAATCCGCAAGTGGTA
1 AAAATTTAAATGGCCCAAAGGTGAGTGAATCCGCAAGTGGTA
*
38621 AAAATTTAAATGGCCCAAAGGTGAGTGAATCTGCAAGTGGTA
1 AAAATTTAAATGGCCCAAAGGTGAGTGAATCCGCAAGTGGTA
38663 AAAAT
1 AAAAT
38668 AGAGTGAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.22
Consensus pattern (42 bp):
AAAATTTAAATGGCCCAAAGGTGAGTGAATCCGCAAGTGGTA
Found at i:41671 original size:42 final size:42
Alignment explanation
Indices: 41612--41700 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
41602 GAAAAAATTC
*
41612 AAAATTTAAATGGCCCAAAGGTGAGTGAATCTGCAAGTGGTA
1 AAAATTTAAATGGCCCAAACGTGAGTGAATCTGCAAGTGGTA
41654 AAAATTTAAATGGCCCAAACGTGAGTGAATCTGCAAGTGGTA
1 AAAATTTAAATGGCCCAAACGTGAGTGAATCTGCAAGTGGTA
41696 AAAAT
1 AAAAT
41701 AGAGTGAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (42 bp):
AAAATTTAAATGGCCCAAACGTGAGTGAATCTGCAAGTGGTA
Found at i:44723 original size:42 final size:42
Alignment explanation
Indices: 44664--44752 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
44654 GAAAAAAGTC
*
44664 AAAATTTAAATGGCCCAAAGGTGAGTGAATCCGCAAGTGGTA
1 AAAATTTAAATGGCCCAAACGTGAGTGAATCCGCAAGTGGTA
**
44706 AAAATTTAAATGGCCCAAACGTGAGTGAATTTGCAAGTGGTA
1 AAAATTTAAATGGCCCAAACGTGAGTGAATCCGCAAGTGGTA
44748 AAAAT
1 AAAAT
44753 AGAGTGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (42 bp):
AAAATTTAAATGGCCCAAACGTGAGTGAATCCGCAAGTGGTA
Found at i:54103 original size:29 final size:28
Alignment explanation
Indices: 54061--54133 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 28
54051 CATGAGATTG
54061 GCACTAAGTGTGCGGGTTCAAAT-TGTATA
1 GCACTAAGTGTGCGGGTTCAAATAT-TA-A
* *
54090 GCACTAAGTGTGCGAGTTCAACTATTAA
1 GCACTAAGTGTGCGGGTTCAAATATTAA
54118 GCACTAAGTGTGCGGG
1 GCACTAAGTGTGCGGG
54134 CTTATTATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 16 0.40
29 23 0.57
30 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (28 bp):
GCACTAAGTGTGCGGGTTCAAATATTAA
Found at i:62845 original size:36 final size:37
Alignment explanation
Indices: 62805--62877 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
62795 TCAAAAACCT
62805 GCAAAACAAACACTCAA-CACTCAAAAAGAAAAATTA
1 GCAAAACAAACACTCAATCACTCAAAAAGAAAAATTA
* ** ** *
62841 GCAAACCTCACTGTTAATCACTCAAAAAGAAAAATTA
1 GCAAAACAAACACTCAATCACTCAAAAAGAAAAATTA
62878 AATTCTCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
36 11 0.37
37 19 0.63
ACGTcount: A:0.55, C:0.22, G:0.07, T:0.16
Consensus pattern (37 bp):
GCAAAACAAACACTCAATCACTCAAAAAGAAAAATTA
Found at i:63866 original size:18 final size:18
Alignment explanation
Indices: 63843--63878 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
63833 AGATTAAAAA
63843 AATCAGA-TCACAAAGAAT
1 AATCAGATTCA-AAAGAAT
63861 AATCAGATTCAAAAGAAT
1 AATCAGATTCAAAAGAAT
63879 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.19
Consensus pattern (18 bp):
AATCAGATTCAAAAGAAT
Done.