Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold959
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: 22650
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Found at i:8077 original size:46 final size:45
Alignment explanation
Indices: 7910--8078 Score: 200
Period size: 46 Copynumber: 3.7 Consensus size: 45
7900 GGTTGAGCAT
*
7910 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
* * * * * * *
7954 TCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTA-ACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATGGATGCAACGC
7998 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC
*
8046 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
8079 GGGCGGGTTA
Statistics
Matches: 103, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
43 4 0.04
44 31 0.30
46 63 0.61
47 2 0.02
48 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
Found at i:12826 original size:27 final size:27
Alignment explanation
Indices: 12795--12972 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12785 TAAATTGTAC
12795 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
12822 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12848 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
12876 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
12904 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12931 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
12958 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12973 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:12909 original size:82 final size:81
Alignment explanation
Indices: 12796--12951 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12786 AAATTGTACA
* *
12796 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
12860 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
12877 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
12942 TGCGAGTTGA
65 TGCGAATTGA
12952 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:12963 original size:82 final size:81
Alignment explanation
Indices: 12792--12972 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
12782 GATTAAATTG
* *
12792 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
12857 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
12873 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
12937 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
12955 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
12973 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:20922 original size:27 final size:27
Alignment explanation
Indices: 20891--21068 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
20881 TAAATTGTAC
20891 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
20918 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20944 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
20972 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
21000 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21027 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
21054 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21069 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:21005 original size:82 final size:81
Alignment explanation
Indices: 20892--21047 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
20882 AAATTGTACA
* *
20892 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
20956 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
20973 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
21038 TGCGAGTTGA
65 TGCGAATTGA
21048 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:21059 original size:82 final size:81
Alignment explanation
Indices: 20888--21068 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
20878 GATTAAATTG
* *
20888 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
20953 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
20969 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
21033 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
21051 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
21069 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.