Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2386
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: 7707
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Found at i:2099 original size:13 final size:13
Alignment explanation
Indices: 2081--2124 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
2071 CATGGGACAT
2081 TGTATCGATACAA
1 TGTATCGATACAA
2094 TGTATCGAT----
1 TGTATCGATACAA
2103 TGTATCGATACAA
1 TGTATCGATACAA
2116 TGTATCGAT
1 TGTATCGAT
2125 TGTATCGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
9 9 0.33
13 18 0.67
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2107 original size:22 final size:22
Alignment explanation
Indices: 2079--2136 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
2069 TACATGGGAC
2079 ATTGTATCGATACAATGTATCG
1 ATTGTATCGATACAATGTATCG
2101 ATTGTATCGATACAATGTATCG
1 ATTGTATCGATACAATGTATCG
2123 ATTGTATCGATACA
1 ATTGTATCGATACA
2137 TAGTGAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (22 bp):
ATTGTATCGATACAATGTATCG
Found at i:2212 original size:43 final size:42
Alignment explanation
Indices: 2150--2243 Score: 179
Period size: 43 Copynumber: 2.2 Consensus size: 42
2140 TGAAAAGTTT
2150 TGATACATTATGCCCAACGGCTATAAATTTCAAATGCATGTA
1 TGATACATTATGCCCAACGGCTATAAATTTCAAATGCATGTA
2192 TCGATACATTATGCCCAACGGCTATAAATTTCAAATGCATGTA
1 T-GATACATTATGCCCAACGGCTATAAATTTCAAATGCATGTA
2235 TGATACATT
1 TGATACATT
2244 GTGAAAAGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 9 0.18
43 42 0.82
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (42 bp):
TGATACATTATGCCCAACGGCTATAAATTTCAAATGCATGTA
Found at i:4932 original size:106 final size:106
Alignment explanation
Indices: 4747--4960 Score: 428
Period size: 106 Copynumber: 2.0 Consensus size: 106
4737 CAAAAGTATT
4747 AACACTTATGAAAAAGGATCCAAGAAAATTTGGGTACCTAAAACCAAGACTTGATTCTTGTGCTT
1 AACACTTATGAAAAAGGATCCAAGAAAATTTGGGTACCTAAAACCAAGACTTGATTCTTGTGCTT
4812 GTAGGAGGTAGAGCATTGCTACAAGGCAAAGGAATCAAAGA
66 GTAGGAGGTAGAGCATTGCTACAAGGCAAAGGAATCAAAGA
4853 AACACTTATGAAAAAGGATCCAAGAAAATTTGGGTACCTAAAACCAAGACTTGATTCTTGTGCTT
1 AACACTTATGAAAAAGGATCCAAGAAAATTTGGGTACCTAAAACCAAGACTTGATTCTTGTGCTT
4918 GTAGGAGGTAGAGCATTGCTACAAGGCAAAGGAATCAAAGA
66 GTAGGAGGTAGAGCATTGCTACAAGGCAAAGGAATCAAAGA
4959 AA
1 AA
4961 AATTTTTGGT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 108 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.22
Consensus pattern (106 bp):
AACACTTATGAAAAAGGATCCAAGAAAATTTGGGTACCTAAAACCAAGACTTGATTCTTGTGCTT
GTAGGAGGTAGAGCATTGCTACAAGGCAAAGGAATCAAAGA
Done.