Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3266
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: 18531
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:4441 original size:29 final size:29
Alignment explanation
Indices: 4408--4463 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
4398 ACTTCATTCT
4408 TTTTGGGTATCACAAATATGCTAAAAGCG
1 TTTTGGGTATCACAAATATGCTAAAAGCG
4437 TTTTGGGTATCACAAATATGCTAAAAG
1 TTTTGGGTATCACAAATATGCTAAAAG
4464 TAGGTTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (29 bp):
TTTTGGGTATCACAAATATGCTAAAAGCG
Found at i:10957 original size:56 final size:56
Alignment explanation
Indices: 10851--10957 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 56
10841 GTGTTAACCT
* * * *
10851 TTTGAAGAGTTCCTTGTATATTATAAATCACGCGCATTCTATGCATGTGTTGTTTA
1 TTTGAAGAGTTCCTTGAAAATTATAAATCACGCGCATGCTATGCACGTGTTGTTTA
* * * *
10907 TTTGAAGGGTTCCTTGAAAATTGTAAATTACGCGCATGCTATGCGCGTGTT
1 TTTGAAGAGTTCCTTGAAAATTATAAATCACGCGCATGCTATGCACGTGTT
10958 TTCCATTTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 43 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (56 bp):
TTTGAAGAGTTCCTTGAAAATTATAAATCACGCGCATGCTATGCACGTGTTGTTTA
Found at i:11087 original size:66 final size:66
Alignment explanation
Indices: 10981--11112 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
10971 TGCCAAAGAT
10981 GGTTTCACATGTCTCATTGCATGCACGTGTAATGTTACACTCGTTAATATATGTGTCTTGATCTA
1 GGTTTCACATGTCTCATTGCATGCACGTGTAATGTTACACTCGTTAATATATGTGTCTTGATCTA
11046 A
66 A
11047 GGTTTCACATGTCTCATTGCATGCACGTGTAATGTTACACTCGTTAATATATGTGTCTTGATCTA
1 GGTTTCACATGTCTCATTGCATGCACGTGTAATGTTACACTCGTTAATATATGTGTCTTGATCTA
11112 A
66 A
11113 AACTTACAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (66 bp):
GGTTTCACATGTCTCATTGCATGCACGTGTAATGTTACACTCGTTAATATATGTGTCTTGATCTA
A
Found at i:13640 original size:40 final size:41
Alignment explanation
Indices: 13596--13678 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 41
13586 TTTTTTTTTG
*
13596 CGCATGTTTTGACTGAT-TACATAGTATTCTTAGAATATGT
1 CGCATGTTTTGACTGATATACATAGCATTCTTAGAATATGT
* *
13636 CGCATGTTTTGACTGCTCATACGTAGCATTCTTAGAATATGT
1 CGCATGTTTTGACTGAT-ATACATAGCATTCTTAGAATATGT
13678 C
1 C
13679 AATTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 16 0.42
42 22 0.58
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (41 bp):
CGCATGTTTTGACTGATATACATAGCATTCTTAGAATATGT
Found at i:13741 original size:11 final size:11
Alignment explanation
Indices: 13725--13765 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
13715 AAAATGTAAA
13725 AAAATAATTTT
1 AAAATAATTTT
13736 AAAATAATTTT
1 AAAATAATTTT
13747 ATATAA-AATTTT
1 A-A-AATAATTTT
13759 AAAATAA
1 AAAATAA
13766 GTAATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 8 0.30
13 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:13780 original size:22 final size:23
Alignment explanation
Indices: 13730--13784 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
13720 GTAAAAAAAT
**
13730 AATTTTAAAATAATTTTATATAA
1 AATTTTAAAATAATAATATATAA
13753 AATTTTAAAATAAGTAAT-TAT-A
1 AATTTTAAAATAA-TAATATATAA
13775 AATTTTAAAA
1 AATTTTAAAA
13785 AGTTGAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.38
23 16 0.55
24 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTTTAAAATAATAATATATAA
Found at i:17305 original size:21 final size:21
Alignment explanation
Indices: 17279--17321 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
17269 TCACATGGGT
17279 CCAACTAATCCAGGTGATATG
1 CCAACTAATCCAGGTGATATG
*
17300 CCAACTAATCCTGGTGATATG
1 CCAACTAATCCAGGTGATATG
17321 C
1 C
17322 TTTCTTCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
CCAACTAATCCAGGTGATATG
Done.