Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1148
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: 26886
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:3739 original size:22 final size:21
Alignment explanation
Indices: 3701--3757 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
3691 ATTTTAATAT
** *
3701 AAATAAAAGTTGGAAAGTAAA
1 AAATAAAAGTTAAAAAGGAAA
3722 AAATAAATAGTTAAAAAGGAAA
1 AAATAAA-AGTTAAAAAGGAAA
* *
3744 GAATATAAGATTAA
1 AAATAAAAG-TTAA
3758 TGTAATTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.63, C:0.00, G:0.16, T:0.21
Consensus pattern (21 bp):
AAATAAAAGTTAAAAAGGAAA
Found at i:15333 original size:13 final size:13
Alignment explanation
Indices: 15315--15339 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15305 GAGGTGAGAA
15315 AAGAAGAAGAAAG
1 AAGAAGAAGAAAG
15328 AAGAAGAAGAAA
1 AAGAAGAAGAAA
15340 AAAAAATTGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAAG
Found at i:22102 original size:2 final size:2
Alignment explanation
Indices: 22095--22126 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
22085 ACATACATAG
*
22095 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22127 TTTTTCCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24345 original size:13 final size:13
Alignment explanation
Indices: 24327--24357 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
24317 ACATTTCTTC
24327 ATGTATCGATACA
1 ATGTATCGATACA
24340 ATGTATCGATACA
1 ATGTATCGATACA
*
24353 TTGTA
1 ATGTA
24358 CCATGTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:24428 original size:21 final size:21
Alignment explanation
Indices: 24402--24457 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
24392 TTGCCAATTT
**
24402 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
24423 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
24442 CATGTATCGATACAAT
1 CATGTATCGATACAAT
24458 GTATCGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 13 0.42
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:24461 original size:13 final size:13
Alignment explanation
Indices: 24443--24469 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24433 TACATTGAAC
24443 ATGTATCGATACA
1 ATGTATCGATACA
24456 ATGTATCGATACA
1 ATGTATCGATACA
24469 A
1 A
24470 GGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:24625 original size:20 final size:20
Alignment explanation
Indices: 24600--24653 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
24590 TTTACTTAAA
24600 CATGTATCGATACAAGGCAG
1 CATGTATCGATACAAGGCAG
24620 CATGTATCGATACAAGGCAG
1 CATGTATCGATACAAGGCAG
24640 CATGTATCGATACA
1 CATGTATCGATACA
24654 TCTGAGTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
CATGTATCGATACAAGGCAG
Found at i:24639 original size:165 final size:166
Alignment explanation
Indices: 24456--24762 Score: 589
Period size: 166 Copynumber: 1.9 Consensus size: 166
24446 TATCGATACA
24456 ATGTATCGATACAAGGCAGCATGTATCGATACATCTGAGTGTGTATCGATACATTCAAGGGTTTT
1 ATGTATCGATACAAGGCAGCATGTATCGATACATCTGAGTGTGTATCGATACATTCAAGGGTTTT
*
24521 -GACCTTTTTCTCCTAAGTCAACCATAATGTATCGATACAATTACCTATGTATCGATACTTTGAG
66 GGACCTTTTTATCCTAAGTCAACCATAATGTATCGATACAATTACCTATGTATCGATACTTTGAG
*
24585 TATGTTTTACTTAAACATGTATCGATACAAGGCAGC
131 CATGTTTTACTTAAACATGTATCGATACAAGGCAGC
24621 ATGTATCGATACAAGGCAGCATGTATCGATACATCTGAGTGTGTATCGATACATTCAAGGGTTTT
1 ATGTATCGATACAAGGCAGCATGTATCGATACATCTGAGTGTGTATCGATACATTCAAGGGTTTT
24686 GGACCTTTTTATCCTAAGTCAACCATAATGTATCGATACAATTACCTATGTATCGATACTTTGAG
66 GGACCTTTTTATCCTAAGTCAACCATAATGTATCGATACAATTACCTATGTATCGATACTTTGAG
24751 CATGTTTTACTT
131 CATGTTTTACTT
24763 GAAAACTCTT
Statistics
Matches: 139, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
165 65 0.47
166 74 0.53
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (166 bp):
ATGTATCGATACAAGGCAGCATGTATCGATACATCTGAGTGTGTATCGATACATTCAAGGGTTTT
GGACCTTTTTATCCTAAGTCAACCATAATGTATCGATACAATTACCTATGTATCGATACTTTGAG
CATGTTTTACTTAAACATGTATCGATACAAGGCAGC
Done.