Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold246
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: 24093
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Found at i:1819 original size:27 final size:27
Alignment explanation
Indices: 1788--1965 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1778 TAAATTGTAC
1788 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
1815 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1841 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
1869 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
1897 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1924 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
1951 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
1966 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:1902 original size:82 final size:81
Alignment explanation
Indices: 1789--1944 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
1779 AAATTGTACA
* *
1789 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
1853 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
1870 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
1935 TGCGAGTTGA
65 TGCGAATTGA
1945 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:1956 original size:82 final size:81
Alignment explanation
Indices: 1785--1965 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
1775 GATTAAATTG
* *
1785 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
1850 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
1866 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
1930 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
1948 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
1966 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:9935 original size:27 final size:27
Alignment explanation
Indices: 9904--10081 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
9894 TAAATTGTAC
9904 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
9931 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
9957 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
9985 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
10013 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10040 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10067 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10082 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:10018 original size:82 final size:81
Alignment explanation
Indices: 9905--10060 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
9895 AAATTGTACA
* *
9905 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
9969 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
9986 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
10051 TGCGAGTTGA
65 TGCGAATTGA
10061 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:10072 original size:82 final size:81
Alignment explanation
Indices: 9901--10081 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
9891 GATTAAATTG
* *
9901 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
9966 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
9982 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
10046 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
10064 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
10082 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:20250 original size:23 final size:23
Alignment explanation
Indices: 20216--20273 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
20206 ACTTGAATCG
*
20216 CTATTAGCAGCTTTGCTGCGTTA
1 CTATTAGCAGCTTTGCTACGTTA
* * *
20239 GTATTAGTAGCTTTGCTATGTTA
1 CTATTAGCAGCTTTGCTACGTTA
20262 CTATTAGCAGCT
1 CTATTAGCAGCT
20274 ATGTTACGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (23 bp):
CTATTAGCAGCTTTGCTACGTTA
Found at i:20472 original size:33 final size:34
Alignment explanation
Indices: 20415--20486 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
20405 ATAGGCCCAC
* * * *
20415 ACTGTTACTGCATATGGCTTAGGCCCAGACTG-T
1 ACTGTTACTGAATAGGGCTCAGGCCCAGACCGTT
* *
20448 ACTGTTATTGAATAGGGCTCAGGCCTAGACCGTT
1 ACTGTTACTGAATAGGGCTCAGGCCCAGACCGTT
20482 ACTGT
1 ACTGT
20487 ATGCACTGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (34 bp):
ACTGTTACTGAATAGGGCTCAGGCCCAGACCGTT
Found at i:21824 original size:40 final size:40
Alignment explanation
Indices: 21753--21898 Score: 206
Period size: 40 Copynumber: 3.7 Consensus size: 40
21743 TACCAGCTCG
* * * *
21753 TAGCCTGTGGGTCTCT-AGCCCGGATAGCATTCTAGCACGA
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCTAGCA-TA
21793 -AGCCTGCGGGTCTTTAAGCCCGGATAACATTCTAGCATA
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCTAGCATA
* * *
21832 TAGCTTGCGGGTCTTTAAGCCCGGATAACATTCCAGTATA
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCTAGCATA
21872 TAGCCTGCGGGTCTTTAAGCCCGGATA
1 TAGCCTGCGGGTCTTTAAGCCCGGATA
21899 CAATTCTTCA
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
39 14 0.15
40 82 0.85
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (40 bp):
TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCTAGCATA
Found at i:23191 original size:15 final size:15
Alignment explanation
Indices: 23159--23187 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23149 ATTTTTAGTG
23159 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
23174 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
23188 ATTTTCGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Done.