Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2220
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: 35758
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2246 original size:56 final size:56
Alignment explanation
Indices: 2184--2299 Score: 223
Period size: 56 Copynumber: 2.1 Consensus size: 56
2174 TTAAAATAAG
2184 AAAAAATCATATGGCTTCTGAAAATCAAACATCTCAAACTCAGTACACCATACAAC
1 AAAAAATCATATGGCTTCTGAAAATCAAACATCTCAAACTCAGTACACCATACAAC
*
2240 AAAAAATCATATGGCTTCTGAAAATCAAACATCTCAAACTCAGTATACCATACAAC
1 AAAAAATCATATGGCTTCTGAAAATCAAACATCTCAAACTCAGTACACCATACAAC
2296 AAAA
1 AAAA
2300 CCAGAAATAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.48, C:0.23, G:0.07, T:0.22
Consensus pattern (56 bp):
AAAAAATCATATGGCTTCTGAAAATCAAACATCTCAAACTCAGTACACCATACAAC
Found at i:5260 original size:12 final size:13
Alignment explanation
Indices: 5200--5265 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
5190 TAACCTTTTC
5200 TTATAAAGATATT
1 TTATAAAGATATT
5213 TTATAAAGATATT
1 TTATAAAGATATT
* * * *
5226 TAAGTAGATATTTT
1 TTA-TAAAGATATT
5240 TTATAAAGATATT
1 TTATAAAGATATT
*
5253 TT-TAAAGAAATT
1 TTATAAAGATATT
5265 T
1 T
5266 ATACATAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
12 10 0.23
13 24 0.56
14 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (13 bp):
TTATAAAGATATT
Found at i:11804 original size:12 final size:11
Alignment explanation
Indices: 11776--11808 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
11766 ATTATACTTA
11776 TTTTC-TTTTC
1 TTTTCTTTTTC
11786 TTTTCTTTTTC
1 TTTTCTTTTTC
11797 TCTTTCTTTTTC
1 T-TTTCTTTTTC
11809 GTTATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 6 0.29
12 10 0.48
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:14138 original size:3 final size:3
Alignment explanation
Indices: 14132--14156 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14122 TAGAAGAAGA
14132 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
14157 AGATGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:20839 original size:42 final size:42
Alignment explanation
Indices: 20780--20862 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
20770 GAGTGTCTTC
20780 GCTTTTGAATTAACCTTCCCAACCGGTTCAGAGGCAATATTT
1 GCTTTTGAATTAACCTTCCCAACCGGTTCAGAGGCAATATTT
20822 GCTTTTGAATTAACCTTCCCAACCGGTTCAGAGGCAATATT
1 GCTTTTGAATTAACCTTCCCAACCGGTTCAGAGGCAATATT
20863 GGGTGACTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (42 bp):
GCTTTTGAATTAACCTTCCCAACCGGTTCAGAGGCAATATTT
Found at i:27133 original size:22 final size:24
Alignment explanation
Indices: 27108--27153 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27098 ATAATCATAC
*
27108 TGCA-GACA-TCATAACAAAAAAA
1 TGCAGGACAGTCATAAAAAAAAAA
27130 TGCAGGACAGTCATAAAAAAAAAA
1 TGCAGGACAGTCATAAAAAAAAAA
27154 ATGGATGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 4 0.19
24 13 0.62
ACGTcount: A:0.59, C:0.15, G:0.13, T:0.13
Consensus pattern (24 bp):
TGCAGGACAGTCATAAAAAAAAAA
Done.