Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2553
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: 6108
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Found at i:60 original size:34 final size:35
Alignment explanation
Indices: 1--112 Score: 140
Period size: 34 Copynumber: 3.3 Consensus size: 35
* * *
1 GATTAAATGAGAAATTTGGTA-GCTTACCATTGTT
1 GATTAAATGGGAGATTTAGTAGGCTTACCATTGTT
*
35 GATTAAATGGGTGATTTAGT-GGCTTACCATTGTT
1 GATTAAATGGGAGATTTAGTAGGCTTACCATTGTT
* * *
69 GACTAAATGGGAGATTTGGTAGG-TTGCCATTGTT
1 GATTAAATGGGAGATTTAGTAGGCTTACCATTGTT
103 GATTAAATGG
1 GATTAAATGG
113 TGGTTTTTAC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 65 0.97
35 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.38
Consensus pattern (35 bp):
GATTAAATGGGAGATTTAGTAGGCTTACCATTGTT
Found at i:903 original size:20 final size:22
Alignment explanation
Indices: 866--911 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
856 TTATTTTAAG
866 TATTTTAATTAGATAAATTT-A
1 TATTTTAATTAGATAAATTTGA
*
887 TATTTTTATTA-ATAAATTTGA
1 TATTTTAATTAGATAAATTTGA
908 TATT
1 TATT
912 AATTTGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TATTTTAATTAGATAAATTTGA
Found at i:1681 original size:8 final size:8
Alignment explanation
Indices: 1664--1700 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
1654 TTAAGTTAAA
1664 TTAATTTT
1 TTAATTTT
1672 TT-ATTTT
1 TTAATTTT
*
1679 TTTA-TTT
1 TTAATTTT
1686 TTAATTTT
1 TTAATTTT
1694 TTAATTT
1 TTAATTT
1701 GAATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
7 13 0.50
8 13 0.50
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTAATTTT
Found at i:1687 original size:15 final size:15
Alignment explanation
Indices: 1664--1700 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1654 TTAAGTTAAA
*
1664 TTAATTTTTTATTTT
1 TTAATTTTTAATTTT
*
1679 TTTATTTTTAATTTT
1 TTAATTTTTAATTTT
1694 TTAATTT
1 TTAATTT
1701 GAATAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTAATTTTTAATTTT
Found at i:2432 original size:19 final size:19
Alignment explanation
Indices: 2408--2444 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2398 AGTTTGGTTA
* *
2408 ATCAATTTTTTTTATTTTG
1 ATCAATTTATTTAATTTTG
2427 ATCAATTTATTTAATTTT
1 ATCAATTTATTTAATTTT
2445 TTAAGTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (19 bp):
ATCAATTTATTTAATTTTG
Found at i:3254 original size:33 final size:33
Alignment explanation
Indices: 3217--3285 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
3207 CACCTGCAGA
3217 TATAAACAAATTGAATATCTAATCATATTAAAT
1 TATAAACAAATTGAATATCTAATCATATTAAAT
3250 TATAAACAAATTGAATATCTAATCATATTAAAT
1 TATAAACAAATTGAATATCTAATCATATTAAAT
3283 TAT
1 TAT
3286 TATTTACCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.38
Consensus pattern (33 bp):
TATAAACAAATTGAATATCTAATCATATTAAAT
Found at i:3881 original size:16 final size:15
Alignment explanation
Indices: 3849--3890 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3839 TGCTTTTATT
3849 AAAATTATATAATAA
1 AAAATTATATAATAA
3864 AAAATTA-ATATATAA
1 AAAATTATATA-ATAA
*
3879 AAATTTATATAA
1 AAAATTATATAA
3891 AGATAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 18 0.75
16 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATTATATAATAA
Found at i:5890 original size:11 final size:11
Alignment explanation
Indices: 5873--5914 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
5863 TCACAATTCA
5873 TATATTTATAT
1 TATATTTATAT
*
5884 AATATTTAT-T
1 TATATTTATAT
5894 TATATATTATAAT
1 TATAT-TTAT-AT
5907 TATATTTA
1 TATATTTA
5915 ACATGTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 5 0.19
11 12 0.46
12 3 0.12
13 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Done.