Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2829
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: 23425
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7510 original size:20 final size:20
Alignment explanation
Indices: 7485--7528 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
7475 TCGTTTCCAG
*
7485 CTCACTCGAGCTCAAGTCAA
1 CTCACTCAAGCTCAAGTCAA
*
7505 CTCACTCAAGCTCAATTCAA
1 CTCACTCAAGCTCAAGTCAA
7525 CTCA
1 CTCA
7529 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.09, T:0.23
Consensus pattern (20 bp):
CTCACTCAAGCTCAAGTCAA
Found at i:9064 original size:13 final size:15
Alignment explanation
Indices: 9048--9080 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
9038 AAAAAATTTC
9048 AAAAAAAAG-GA-AA
1 AAAAAAAAGTGACAA
9061 AAAAAAAAGTGACAA
1 AAAAAAAAGTGACAA
9076 AAAAA
1 AAAAA
9081 TCGAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAAAAGTGACAA
Found at i:10213 original size:48 final size:47
Alignment explanation
Indices: 10134--10239 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
10124 GAGTGTCATG
*
10134 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
10182 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
10230 GAAAAAGAAA
1 GAAAAAGAAA
10240 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:11955 original size:20 final size:20
Alignment explanation
Indices: 11909--11955 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
11899 AGCTCGTTTC
*
11909 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
11929 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
11949 CAGCTCA
1 CAGCTCA
11956 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:14616 original size:48 final size:47
Alignment explanation
Indices: 14537--14642 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
14527 GAGTGTCATG
*
14537 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
14585 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
14633 GAAAAAGAAA
1 GAAAAAGAAA
14643 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:16358 original size:20 final size:20
Alignment explanation
Indices: 16312--16358 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
16302 AGCTCGTTTC
*
16312 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
16332 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
16352 CAGCTCA
1 CAGCTCA
16359 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17911 original size:18 final size:18
Alignment explanation
Indices: 17854--17937 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 18
17844 TGTATTGAAT
* **
17854 AAAAAAAGAAAAATTTCA
1 AAAAAAAAAAAAATGACA
* **
17872 AAAAAAATAAAAAT-AGGG
1 AAAAAAAAAAAAATGA-CA
17890 AAAAAAAAAAAAATGACA
1 AAAAAAAAAAAAATGACA
**
17908 AAAAAAGTAAAAA-GA-A
1 AAAAAAAAAAAAATGACA
17924 AAAGAAAAAAAAAA
1 AAA-AAAAAAAAAA
17938 AGTGAAAGTC
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
16 4 0.08
17 10 0.19
18 37 0.71
19 1 0.02
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (18 bp):
AAAAAAAAAAAAATGACA
Found at i:17919 original size:23 final size:23
Alignment explanation
Indices: 17892--17936 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
17882 AAATAGGGAA
* *
17892 AAAAAAAAAAATGACAAAAAAAGT
1 AAAAAGAAAAA-GAAAAAAAAAGT
17916 AAAAAGAAAAAGAAAAAAAAA
1 AAAAAGAAAAAGAAAAAAAAA
17937 AAGTGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.04
Consensus pattern (23 bp):
AAAAAGAAAAAGAAAAAAAAAGT
Found at i:17925 original size:13 final size:13
Alignment explanation
Indices: 17907--17940 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
17897 AAAAAATGAC
17907 AAAAAAAGTAAAA
1 AAAAAAAGTAAAA
*
17920 AGAAAAAG-AAAA
1 AAAAAAAGTAAAA
17932 AAAAAAAGT
1 AAAAAAAGT
17941 GAAAGTCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (13 bp):
AAAAAAAGTAAAA
Found at i:20747 original size:20 final size:21
Alignment explanation
Indices: 20700--20747 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
20690 TAGCTCGTTC
20700 CAGCTCACTCGAAGCTCAAGT
1 CAGCTCACTCGAAGCTCAAGT
* *
20721 CAACTCACTC-AAGCTCAATT
1 CAGCTCACTCGAAGCTCAAGT
20741 CAGCTCA
1 CAGCTCA
20748 ATCTTAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.21
Consensus pattern (21 bp):
CAGCTCACTCGAAGCTCAAGT
Done.