Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1004
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: 4183
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Found at i:1987 original size:17 final size:17
Alignment explanation
Indices: 1965--1998 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1955 GATAAAGTGT
1965 TTGAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAA
1982 TTGAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAA
1999 AAATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
TTGAAAAAAAAAAAAAA
Found at i:2030 original size:21 final size:21
Alignment explanation
Indices: 2006--2062 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1996 AAAAAATTTA
2006 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2027 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2048 AATGTATCGATACAT
1 AATGTATCGATACAT
2063 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2142 original size:19 final size:19
Alignment explanation
Indices: 2118--2185 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2108 AATTCAACAA
2118 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2137 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2152 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2169 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2186 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2157 original size:13 final size:13
Alignment explanation
Indices: 2139--2163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2129 ACATAAGTTT
2139 TGTATCGATACAA
1 TGTATCGATACAA
2152 TGTATCGATACA
1 TGTATCGATACA
2164 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2161 original size:32 final size:32
Alignment explanation
Indices: 2120--2182 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2110 TTCAACAATT
*
2120 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2152 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2183 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2243 original size:13 final size:13
Alignment explanation
Indices: 2225--2250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2215 CATTTTTCTG
2225 TGTATCGATACAT
1 TGTATCGATACAT
2238 TGTATCGATACAT
1 TGTATCGATACAT
2251 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2247 original size:33 final size:33
Alignment explanation
Indices: 2205--2271 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2195 GCCAAGGAAA
***
2205 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2238 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2271 T
1 T
2272 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Done.