Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1369
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: 23401
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:325 original size:23 final size:23
Alignment explanation
Indices: 274--325 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
264 TATTACATAC
274 AAAGG-GAGCTTATATATCATTA
1 AAAGGAGAGCTTATATATCATTA
296 AAA--AGAGC-TATTATATCATTA
1 AAAGGAGAGCTTA-TATATCATTA
317 AAAGGAGAG
1 AAAGGAGAG
326 AATTACACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.08
21 17 0.65
22 3 0.12
23 4 0.15
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (23 bp):
AAAGGAGAGCTTATATATCATTA
Found at i:7893 original size:20 final size:20
Alignment explanation
Indices: 7870--7916 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7860 GGGTTAAGAT
*
7870 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
7890 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
7910 TGAGCTG
1 TGAGCTG
7917 GAAACGAGCT
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:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:14171 original size:20 final size:20
Alignment explanation
Indices: 14148--14201 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
14138 AGTTTTTCCC
*
14148 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
14168 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
14188 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
14202 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:14183 original size:30 final size:30
Alignment explanation
Indices: 14148--14221 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
14138 AGTTTTTCCC
14148 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
14178 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
14208 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
14222 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:14211 original size:20 final size:20
Alignment explanation
Indices: 14148--14212 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
14138 AGTTTTTCCC
* * * *
14148 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
14168 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
14187 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
14208 AGCTC
1 AGCTC
14213 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:16891 original size:6 final size:6
Alignment explanation
Indices: 16863--17002 Score: 64
Period size: 6 Copynumber: 22.3 Consensus size: 6
16853 CCATTGAGCG
* * * * * * *
16863 AGAAAA GGAAAA AGAGAT TGAAAA AGAAAT TGAAAGA AAACAAA AAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGA-AAA A-GAAAA
* * * * * * ** *
16914 TGAAAA AGAAAA AGAAAT TGCAAA AGAAAA AGAAAT CGAAAA AGTGAG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
* *
16962 AGAAAA AGAAAA TGAAGAAA AGAAAA TTGAAAA AGAAAA AG
1 AGAAAA AGAAAA AG-A-AAA AGAAAA -AGAAAA AGAAAA AG
17003 CGAAAAAAGA
Statistics
Matches: 92, Mismatches: 36, Indels: 12
0.66 0.26 0.09
Matches are distributed among these distances:
6 72 0.78
7 13 0.14
8 7 0.08
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (6 bp):
AGAAAA
Found at i:16891 original size:18 final size:18
Alignment explanation
Indices: 16864--17002 Score: 104
Period size: 18 Copynumber: 7.7 Consensus size: 18
16854 CATTGAGCGA
* *
16864 GAAAAGGAAAAAGAGATT
1 GAAAAAGAAAAAGAAATT
**
16882 GAAAAAGAAATTGAAA--
1 GAAAAAGAAAAAGAAATT
* *
16898 G-AAAACAAAAAGAAAAT
1 GAAAAAGAAAAAGAAATT
16915 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
* *
16933 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATT
** * **
16951 GAAAAAGTGAGAGAAAAA
1 GAAAAAGAAAAAGAAATT
*
16969 GAAAATGAAGAAAAGAAAATT
1 GAAAAAG-A-AAAAG-AAATT
16990 GAAAAAGAAAAAG
1 GAAAAAGAAAAAG
17003 CGAAAAAAGA
Statistics
Matches: 91, Mismatches: 24, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
15 11 0.12
16 1 0.01
17 1 0.01
18 60 0.66
19 5 0.05
20 4 0.04
21 9 0.10
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:16984 original size:14 final size:13
Alignment explanation
Indices: 16963--17000 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
16953 AAAAGTGAGA
16963 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
16975 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
16990 GAAAAAGAAAA
1 GAAAAAGAAAA
17001 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:17014 original size:21 final size:21
Alignment explanation
Indices: 16964--17014 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
16954 AAAGTGAGAG
*
16964 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
16985 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
17006 AAAAAGAAA
1 AAAAAGAAA
17015 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:17054 original size:33 final size:33
Alignment explanation
Indices: 17017--17079 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
17007 AAAAGAAATT
17017 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
17050 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
17080 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:18879 original size:20 final size:20
Alignment explanation
Indices: 18856--18909 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
18846 AGTTTTTCCC
*
18856 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
18876 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
18896 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
18910 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:18891 original size:30 final size:30
Alignment explanation
Indices: 18856--18929 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
18846 AGTTTTTCCC
18856 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
18886 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
18916 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
18930 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:18919 original size:20 final size:20
Alignment explanation
Indices: 18856--18920 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
18846 AGTTTTTCCC
* * * *
18856 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
18876 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
18895 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
18916 AGCTC
1 AGCTC
18921 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Done.