Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4422
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, 321
Length: 535
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.32
Found at i:39 original size:7 final size:7
Alignment explanation
Indices: 27--128 Score: 78
Period size: 7 Copynumber: 13.9 Consensus size: 7
17 GATATAAGGT
27 TTAGGGG
1 TTAGGGG
34 TTAGGGG
1 TTAGGGG
* *
41 TCAGGGAT
1 TTAGGG-G
49 TTAGGGG
1 TTAGGGG
*
56 TTAGGAG
1 TTAGGGG
63 TTAGGGG
1 TTAGGGG
**
70 TTAGGAA
1 TTAGGGG
*
77 TTTGGGG
1 TTAGGGG
*
84 TCTAGGAGAT
1 T-TAGG-G-G
94 TTAGGGG
1 TTAGGGG
101 TTAGGGG
1 TTAGGGG
*
108 TTAGGGAT
1 TTAGGG-G
*
116 TTAGGGT
1 TTAGGGG
123 TTAGGG
1 TTAGGG
129 TGTCAATTAA
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
7 54 0.72
8 15 0.20
9 5 0.07
10 1 0.01
ACGTcount: A:0.20, C:0.02, G:0.47, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:47 original size:29 final size:29
Alignment explanation
Indices: 15--70 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5 ATTAGGGTTT
* *
15 GGGATATAAGGTTTAGGGGTTAGGGGTCA
1 GGGATATAAGGGTTAGGAGTTAGGGGTCA
* *
44 GGGATTTAGGGGTTAGGAGTTAGGGGT
1 GGGATATAAGGGTTAGGAGTTAGGGGT
71 TAGGAATTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.02, G:0.48, T:0.29
Consensus pattern (29 bp):
GGGATATAAGGGTTAGGAGTTAGGGGTCA
Found at i:51 original size:22 final size:22
Alignment explanation
Indices: 26--133 Score: 110
Period size: 22 Copynumber: 4.8 Consensus size: 22
16 GGATATAAGG
26 TTTAGGGGTTAGGGGTCAGGGA
1 TTTAGGGGTTAGGGGTCAGGGA
* *
48 TTTAGGGGTTAGGAGTTAGGG-
1 TTTAGGGGTTAGGGGTCAGGGA
* ** *
69 GTTAGGAATTTGGGGTCTAGGAGA
1 TTTAGGGGTTAGGGGTC-AGG-GA
*
93 TTTAGGGGTTAGGGGTTAGGGA
1 TTTAGGGGTTAGGGGTCAGGGA
*
115 TTTAGGGTTTAGGGTGTCA
1 TTTAGGGGTTAGGG-GTCA
134 ATTAATGGTA
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
21 11 0.16
22 37 0.55
23 7 0.10
24 12 0.18
ACGTcount: A:0.19, C:0.03, G:0.45, T:0.32
Consensus pattern (22 bp):
TTTAGGGGTTAGGGGTCAGGGA
Found at i:79 original size:29 final size:28
Alignment explanation
Indices: 27--105 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
17 GATATAAGGT
* * *
27 TTAGGGGTTAGGGGTCAGGGATTTAGGGG
1 TTAGGAGTTAGGGGTTAGGAATTT-GGGG
56 TTAGGAGTTAGGGGTTAGGAATTTGGGG
1 TTAGGAGTTAGGGGTTAGGAATTTGGGG
84 TCTAGGAGATTTAGGGGTTAGG
1 T-TAGGAG--TTAGGGGTTAGG
106 GGTTAGGGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 5 0.11
29 27 0.61
31 12 0.27
ACGTcount: A:0.20, C:0.03, G:0.47, T:0.30
Consensus pattern (28 bp):
TTAGGAGTTAGGGGTTAGGAATTTGGGG
Found at i:121 original size:15 final size:15
Alignment explanation
Indices: 34--128 Score: 90
Period size: 15 Copynumber: 6.4 Consensus size: 15
24 GGTTTAGGGG
*
34 TTAGGGGTCAGGGAT
1 TTAGGGGTTAGGGAT
*
49 TTAGGGGTTA-GGAG
1 TTAGGGGTTAGGGAT
*
63 TTAGGGGTTAGGAAT
1 TTAGGGGTTAGGGAT
78 TT-GGGGTCTAGGAGAT
1 TTAGGGGT-TAGG-GAT
*
94 TTAGGGGTTAGGG-G
1 TTAGGGGTTAGGGAT
*
108 TTAGGGATTTAGGG-T
1 TTAGGG-GTTAGGGAT
123 TTAGGG
1 TTAGGG
129 TGTCAATTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
14 24 0.36
15 30 0.45
16 8 0.12
17 5 0.07
ACGTcount: A:0.20, C:0.02, G:0.46, T:0.32
Consensus pattern (15 bp):
TTAGGGGTTAGGGAT
Found at i:129 original size:7 final size:7
Alignment explanation
Indices: 6--129 Score: 63
Period size: 7 Copynumber: 17.0 Consensus size: 7
1 GATTA
6 TTAGGGT
1 TTAGGGT
13 TT-GGGAT
1 TTAGGG-T
* *
20 ATAAGGT
1 TTAGGGT
*
27 TTAGGGG
1 TTAGGGT
*
34 TTAGGGG
1 TTAGGGT
*
41 TCAGGGAT
1 TTAGGG-T
*
49 TTAGGGG
1 TTAGGGT
56 TTAGGAG-
1 TTAGG-GT
*
63 TTAGGGG
1 TTAGGGT
*
70 TTAGGAAT
1 TTAGG-GT
*
78 TTGGGGT
1 TTAGGGT
*
85 CTAGGAGAT
1 TTAGG-G-T
*
94 TTAGGGG
1 TTAGGGT
*
101 TTAGGGG
1 TTAGGGT
108 TTAGGGAT
1 TTAGGG-T
116 TTAGGGT
1 TTAGGGT
123 TTAGGGT
1 TTAGGGT
130 GTCAATTAAT
Statistics
Matches: 90, Mismatches: 18, Indels: 18
0.71 0.14 0.14
Matches are distributed among these distances:
6 4 0.04
7 61 0.68
8 20 0.22
9 5 0.06
ACGTcount: A:0.20, C:0.02, G:0.45, T:0.33
Consensus pattern (7 bp):
TTAGGGT
Done.