Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_452 ID=scaffold_452-JGI_221_v2.0
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: 7308
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.32
Warning! 485 characters in sequence are not A, C, G, or T
Found at i:2902 original size:41 final size:41
Alignment explanation
Indices: 2845--2998 Score: 245
Period size: 41 Copynumber: 3.8 Consensus size: 41
2835 TTATATAAAA
* * * *
2845 CACCGGCATAAAGCCTGCTAGGCACAAAGCCAAATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTAATACATTT
* *
2886 CACCGGCACAGAGCCTGCTAGGCATAGAGCCTGATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTAATACATTT
*
2927 CACCGGCACAGAGCCTGCTAGGCATAGAGCCTAATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTAATACATTT
2968 CACCGGCACAGAGCCTGCTAGGCATAAAGCC
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCC
2999 CGAACTTACA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 105 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.17
Consensus pattern (41 bp):
CACCGGCACAGAGCCTGCTAGGCATAAAGCCTAATACATTT
Found at i:3364 original size:159 final size:159
Alignment explanation
Indices: 3070--3484 Score: 730
Period size: 159 Copynumber: 2.6 Consensus size: 159
3060 AACAATTCAC
* * *
3070 TATAT-TACATTCGGCCATAGCTTATGTAACTTCAAATAATTTATTTCAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
* **
3134 TCTATGCATTCGGCCATAGTTTCTTTCATTTCTCTGCATAACAATTACATATACATTCAGCTATA
66 TATATGCATTCGGCCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATA
3199 GATTAATTCATTTCAATGTATAACAAATA
131 GATTAATTCATTTCAATGTATAACAAATA
3228 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
3293 TATATGCATTCGGCCATAGTTTAAATT-ATTTCTCTGCATAACAATTACATATACATTCAGCTAT
66 TATATGCATTCGGCCATAGTTT-AATTCATTTCTCTGCATAACAATTACATATACATTCAGCTAT
3357 AGATTAATTCATTTCAATGTATAACAAATA
130 AGATTAATTCATTTCAATGTATAACAAATA
3387 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
*
3452 TATA--CATTCGGCCATAGCTTAATTCATTTCTCT
66 TATATGCATTCGGCCATAGTTTAATTCATTTCTCT
3485 CAGATGTCGT
Statistics
Matches: 247, Mismatches: 7, Indels: 7
0.95 0.03 0.03
Matches are distributed among these distances:
156 4 0.02
157 23 0.09
158 5 0.02
159 213 0.86
160 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (159 bp):
TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
TATATGCATTCGGCCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATA
GATTAATTCATTTCAATGTATAACAAATA
Done.