Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1491
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: 12477
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Found at i:1896 original size:27 final size:27
Alignment explanation
Indices: 1865--2042 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1855 TAAATTGTAC
1865 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
1892 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1918 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
1946 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
1974 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2001 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2028 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2043 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:1979 original size:82 final size:81
Alignment explanation
Indices: 1866--2021 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
1856 AAATTGTACA
* *
1866 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
1930 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
1947 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
2012 TGCGAGTTGA
65 TGCGAATTGA
2022 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2033 original size:82 final size:81
Alignment explanation
Indices: 1862--2042 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
1852 GATTAAATTG
* *
1862 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
1927 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
1943 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
2007 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
2025 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2043 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:8545 original size:20 final size:21
Alignment explanation
Indices: 8512--8559 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
8502 TGGTAAGTAG
* *
8512 ATTAGAAAATAAAAGAAG-TGA
1 ATTA-AAAAGAAAAAAAGATGA
8533 ATTAAAAAGAAAAAAAGATGA
1 ATTAAAAAGAAAAAAAGATGA
8554 A-TAAAA
1 ATTAAAA
8560 TAAGGGAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.17
Consensus pattern (21 bp):
ATTAAAAAGAAAAAAAGATGA
Found at i:10097 original size:27 final size:27
Alignment explanation
Indices: 10066--10243 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
10056 TAAATTGTAC
10066 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
10093 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10119 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
10147 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
10175 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10202 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10229 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10244 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:10186 original size:82 final size:81
Alignment explanation
Indices: 10067--10222 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
10057 AAATTGTACA
* *
10067 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
10131 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
10148 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
10213 TGCGAGTTGA
65 TGCGAATTGA
10223 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:10234 original size:82 final size:81
Alignment explanation
Indices: 10063--10243 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
10053 GGATAAATTG
* *
10063 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
10128 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
10144 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
10208 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
10226 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
10244 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.