Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold489
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: 30975
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:50 original size:2 final size:2
Alignment explanation
Indices: 43--71 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33 TTCTTCTTCT
43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
72 TTTTGCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5876 original size:22 final size:23
Alignment explanation
Indices: 5825--5882 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
5815 CAGCTCGTAT
**
5825 GAGCTTACCGTTTCAGCTCTACG
1 GAGCTTACCGTTTCAGCTCTAAA
5848 GAGCTTACCGTTTCAGCTC-AAA
1 GAGCTTACCGTTTCAGCTCTAAA
5870 GAGCTTACCGTTT
1 GAGCTTACCGTTT
5883 ATTCAGCTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCTAAA
Found at i:9149 original size:23 final size:24
Alignment explanation
Indices: 9121--9165 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
9111 AGATTGAGAG
9121 TGAAAAGAA-TGTGAA-AAAGAAAT
1 TGAAAAGAAGT-TGAAGAAAGAAAT
9144 TGAAAAGAAGTTGAAGAAAGAA
1 TGAAAAGAAGTTGAAGAAAGAA
9166 GAAAATGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (24 bp):
TGAAAAGAAGTTGAAGAAAGAAAT
Found at i:10565 original size:12 final size:13
Alignment explanation
Indices: 10543--10571 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
10533 AAGTTTTATT
10543 TTTATTTTATTTA
1 TTTATTTTATTTA
10556 TTTA-TTTATTTA
1 TTTATTTTATTTA
10568 TTTA
1 TTTA
10572 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:17926 original size:20 final size:20
Alignment explanation
Indices: 17901--17955 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
17891 AACTAAAGTA
17901 AGCTAAAAATGAGCTCATTG
1 AGCTAAAAATGAGCTCATTG
* *
17921 AGCTAAGAACGAGCTCATTG
1 AGCTAAAAATGAGCTCATTG
*
17941 AGCTAAAATTGAGCT
1 AGCTAAAAATGAGCT
17956 GAATTGAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (20 bp):
AGCTAAAAATGAGCTCATTG
Found at i:18882 original size:9 final size:9
Alignment explanation
Indices: 18868--18893 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
18858 CGATTTCAAG
18868 AATCAAGAA
1 AATCAAGAA
18877 AATCAAGAA
1 AATCAAGAA
18886 AATCAAGA
1 AATCAAGA
18894 TTTCAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
AATCAAGAA
Found at i:22071 original size:18 final size:17
Alignment explanation
Indices: 22045--22089 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
22035 CTTTATTTCC
22045 TCTTGTTTCTTTTTCAAT
1 TCTT-TTTCTTTTTCAAT
22063 ATCTTTTTCTTTTTCAAT
1 -TCTTTTTCTTTTTCAAT
*
22081 TTTTTTTCT
1 TCTTTTTCT
22090 CAATCTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.32
18 13 0.52
19 4 0.16
ACGTcount: A:0.11, C:0.16, G:0.02, T:0.71
Consensus pattern (17 bp):
TCTTTTTCTTTTTCAAT
Found at i:22120 original size:18 final size:18
Alignment explanation
Indices: 22050--22122 Score: 50
Period size: 18 Copynumber: 4.3 Consensus size: 18
22040 TTTCCTCTTG
* *
22050 TTTCTTTTTCAATATCTT
1 TTTCTTTTTCAATTTCAT
22068 TTTCTTTTTCAA--T--T
1 TTTCTTTTTCAATTTCAT
* * *
22082 TTT-TTTCTCAATCTCAA
1 TTTCTTTTTCAATTTCAT
22099 TTTCTTTTTCAATTTTC-T
1 TTTCTTTTTCAA-TTTCAT
22117 TTTCTT
1 TTTCTT
22123 CATTTTCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
13 7 0.16
14 4 0.09
15 1 0.02
16 1 0.02
17 3 0.07
18 25 0.57
19 3 0.07
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCTTTTTCAATTTCAT
Found at i:22129 original size:27 final size:30
Alignment explanation
Indices: 22067--22135 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
22057 TTCAATATCT
*
22067 TTTTCTTTTTCAATTTTTTTTCTCAATCTCA
1 TTTTCTTTTTCAATTTTCTTTCTC-ATCTCA
*
22098 ATTTCTTTTTCAATTTTCTTT-TC-T-TCA
1 TTTTCTTTTTCAATTTTCTTTCTCATCTCA
22125 TTTTCTTTTTC
1 TTTTCTTTTTC
22136 TCTCACTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
30 2 0.06
31 19 0.54
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTTCTTTTTCAATTTTCTTTCTCATCTCA
Found at i:22162 original size:17 final size:18
Alignment explanation
Indices: 22142--22181 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
22132 TTTCTCTCAC
22142 TTTTCGATTTCTTTTT-T
1 TTTTCGATTTCTTTTTCT
* *
22159 TTTTTGTTTTCTTTTTCT
1 TTTTCGATTTCTTTTTCT
22177 TTTTC
1 TTTTC
22182 ATTACAATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTCGATTTCTTTTTCT
Done.