Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2096
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: 25392
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1754 original size:25 final size:24
Alignment explanation
Indices: 1705--1770 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1695 ACGGAGAAAG
* *
1705 TATTTATAAGAAAAATATTACAAA
1 TATTTATAAGAAAAAGAATACAAA
*
1729 TATTTATAAGAAAAACGAATATAAA
1 TATTTATAAGAAAAA-GAATACAAA
*
1754 T-TTTTTAA-AAAGAAGAA
1 TATTTATAAGAAA-AAGAA
1771 GCTAAAGGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 6 0.17
24 23 0.64
25 7 0.19
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (24 bp):
TATTTATAAGAAAAAGAATACAAA
Found at i:4146 original size:15 final size:16
Alignment explanation
Indices: 4128--4162 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4118 CTTTTTTAGT
4128 TTTATAATTTT-ATAA
1 TTTATAATTTTCATAA
*
4143 TTTATAGTTTTCATAA
1 TTTATAATTTTCATAA
4159 TTTA
1 TTTA
4163 ATTTTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTATAATTTTCATAA
Found at i:18254 original size:23 final size:23
Alignment explanation
Indices: 18187--18257 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
18177 ATCACAATAA
*
18187 TATCATTA-AAAAATACTAAATTGT
1 TATCATTACAAAAATA--AAATTAT
*
18211 T-TTATT-CACAAAA-AAAA-TAT
1 TATCATTACA-AAAATAAAATTAT
18231 TATCATTACAAAAATAAAATTAT
1 TATCATTACAAAAATAAAATTAT
18254 TATC
1 TATC
18258 TTATTATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
20 3 0.08
21 11 0.29
22 6 0.16
23 13 0.34
24 5 0.13
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (23 bp):
TATCATTACAAAAATAAAATTAT
Found at i:20469 original size:15 final size:15
Alignment explanation
Indices: 20449--20505 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
20439 AATTAATATT
20449 AATATTTTAACAATA
1 AATATTTTAACAATA
*
20464 AATATTTATTACAATAA
1 AATATTT-TAACAAT-A
* *
20481 TAATTATATTAATAATA
1 -AA-TATTTTAACAATA
20498 AATATTTT
1 AATATTTT
20506 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 12 0.36
16 8 0.24
17 2 0.06
18 7 0.21
19 4 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAACAATA
Found at i:20635 original size:13 final size:13
Alignment explanation
Indices: 20617--20643 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20607 ACATTAAAAA
20617 CGTTGTAATGAAC
1 CGTTGTAATGAAC
20630 CGTTGTAATGAAC
1 CGTTGTAATGAAC
20643 C
1 C
20644 TGAATTTAGT
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:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (13 bp):
CGTTGTAATGAAC
Found at i:20920 original size:13 final size:14
Alignment explanation
Indices: 20866--20918 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
20856 CCAAGAAAAT
*
20866 AAGTTATTTTTTAA
1 AAGTCATTTTTTAA
20880 AAGTCATTTTTTAA
1 AAGTCATTTTTTAA
* * *
20894 AAATTATTTTTTAG
1 AAGTCATTTTTTAA
20908 AAGTCATTTTT
1 AAGTCATTTTT
20919 AGTGAAACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.55
Consensus pattern (14 bp):
AAGTCATTTTTTAA
Found at i:22043 original size:9 final size:9
Alignment explanation
Indices: 22029--22062 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
22019 GGTATTTTTC
22029 GGTAATTCG
1 GGTAATTCG
22038 GGTAATTCG
1 GGTAATTCG
22047 GGTAATTCG
1 GGTAATTCG
22056 GGTAATT
1 GGTAATT
22063 TTTAACCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (9 bp):
GGTAATTCG
Found at i:22240 original size:12 final size:12
Alignment explanation
Indices: 22223--22247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22213 AGTAATTTCG
22223 GGTCGGTTAACC
1 GGTCGGTTAACC
22235 GGTCGGTTAACC
1 GGTCGGTTAACC
22247 G
1 G
22248 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Done.