Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3472
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: 17906
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2656 original size:23 final size:23
Alignment explanation
Indices: 2630--2697 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 23
2620 GATGGATTAT
*
2630 ATTATTCTGGTGTGTTTGGGAGG
1 ATTATTCTGGTGTGTTTGGGAAG
*
2653 ATTATATGATACTGGTGTGTTTTGGAAG
1 A-T-TAT--T-CTGGTGTGTTTGGGAAG
*
2681 ATTATACTGGTGTGTTT
1 ATTATTCTGGTGTGTTT
2698 TGGTTGGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
23 12 0.32
24 1 0.03
25 3 0.08
26 3 0.08
27 2 0.05
28 16 0.43
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (23 bp):
ATTATTCTGGTGTGTTTGGGAAG
Found at i:2656 original size:28 final size:28
Alignment explanation
Indices: 2603--2686 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
2593 CACTTTGTGC
2603 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
2632 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* * *
2660 GATACTGGTGTGTTTTGGAAGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
2687 CTGGTGTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 32 0.64
29 18 0.36
ACGTcount: A:0.20, C:0.04, G:0.30, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:2938 original size:21 final size:21
Alignment explanation
Indices: 2890--2976 Score: 95
Period size: 21 Copynumber: 4.1 Consensus size: 21
2880 GGCTATACTG
*
2890 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
*
2911 ATTTCAGGCACCTTGTGTGTCGT
1 A--TCAGGCACCTTATGTGTCGT
** *
2934 ATCAGGCACCTCGTGTGTTGT
1 ATCAGGCACCTTATGTGTCGT
*
2955 TTCAGGCA-CTTATGTGTCGT
1 ATCAGGCACCTTATGTGTCGT
2975 AT
1 AT
2977 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 10 0.18
21 26 0.47
23 19 0.35
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (21 bp):
ATCAGGCACCTTATGTGTCGT
Found at i:5355 original size:40 final size:40
Alignment explanation
Indices: 5284--5460 Score: 216
Period size: 40 Copynumber: 4.5 Consensus size: 40
5274 ACCCAAGTAT
*
5284 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
5323 CTTCGGGTCTTAGCCCGGATATAGCAAATCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
5363 CTTCGGGTCTTAGCCCAGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
5403 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
5443 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
5461 TTATCATCCG
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 100 0.86
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:13236 original size:40 final size:40
Alignment explanation
Indices: 13169--13345 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
13159 ACCCAAGTAT
*
13169 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
13208 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
13248 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
13288 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
13328 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
13346 TTATCATCCG
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 104 0.87
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:15213 original size:46 final size:46
Alignment explanation
Indices: 15163--15310 Score: 136
Period size: 46 Copynumber: 3.1 Consensus size: 46
15153 TGGTTGGACC
15163 ATGGCATCAATGTGATATGTGATCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAATGTGATATGTGATCTGTGTAAGACCATAGCTGGGCT
* * * * * * *
15209 ATGGCATCAGAGATATGTGATTACGTGCTTCCGTATAAGACCATATCCGGGAT
1 ATGGCATC----A-ATGTGA-TATGTG-ATCTGTGTAAGACCATAGCTGGGCT
* *
15262 ATGGCATCAGTGTGATATGTGAT-TCGTGTAAGACCATGGCTGGGCT
1 ATGGCATCAATGTGATATGTGATCT-GTGTAAGACCATAGCTGGGCT
15308 ATG
1 ATG
15311 CTACGGTGTG
Statistics
Matches: 78, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
46 28 0.36
47 5 0.06
48 5 0.06
49 1 0.01
50 1 0.01
51 6 0.08
52 5 0.06
53 27 0.35
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (46 bp):
ATGGCATCAATGTGATATGTGATCTGTGTAAGACCATAGCTGGGCT
Done.