Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1518
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: 20306
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3657 original size:98 final size:99
Alignment explanation
Indices: 3391--3686 Score: 495
Period size: 99 Copynumber: 3.0 Consensus size: 99
3381 TCGATTTGAA
* * *
3391 ATTTTGTGTAAGACCCCGTCTGGGATAGAGGCATCGATATTGAATTACATGTAAGACCATGTCTG
1 ATTTCGTGTAAGACCCTGTCTGGGATAGAGGCATCGATATTGAATTACATGTAAGACCACGTCTG
*
3456 GGACATTGGCATTGTACTTGTTTATGAGTATCTG
66 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
* * * *
3490 ATTTCATGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGAATTACATGTAAGATCACATCTG
1 ATTTCGTGTAAGACCCTGTCTGGGATAGAGGCATCGATATTGAATTACATGTAAGACCACGTCTG
3555 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
66 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
* *
3589 ATTTCGTGTAAGA-CCTGTCTAGGATAGAGGCATCGATATTGAATTACATGTAAGACCACGTTTG
1 ATTTCGTGTAAGACCCTGTCTGGGATAGAGGCATCGATATTGAATTACATGTAAGACCACGTCTG
3653 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
66 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
3687 TATCGCTTCG
Statistics
Matches: 183, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 80 0.44
99 103 0.56
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (99 bp):
ATTTCGTGTAAGACCCTGTCTGGGATAGAGGCATCGATATTGAATTACATGTAAGACCACGTCTG
GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
Found at i:11161 original size:99 final size:99
Alignment explanation
Indices: 10866--11162 Score: 504
Period size: 99 Copynumber: 3.0 Consensus size: 99
10856 TCGATCTGAA
* *
10866 ATTTCGTGTAAGACCCTATCTGGGATAGAGGCATCAATATTGAATTACATGTAAGACCACGTTTG
1 ATTTCGTGTAAGACCCTGTCTGGGATAGAGGCATCAATATTGAATTACATGTAAGACCACGTCTG
**
10931 GGACGTTGGCATTGTACTTGTTTATGAGTATCAA
66 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
* * * *
10965 ATTTTGTGTAAGACCCTGTCTGGGACAGAGGCATCAATATTGAATTACATGTAAGATCACATCTG
1 ATTTCGTGTAAGACCCTGTCTGGGATAGAGGCATCAATATTGAATTACATGTAAGACCACGTCTG
11030 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
66 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
* *
11064 ATTTCGTGTAAGACCCTGTCTGGGATAGAGGCATCGATATTGGATTACATGTAAGACCACGTCTG
1 ATTTCGTGTAAGACCCTGTCTGGGATAGAGGCATCAATATTGAATTACATGTAAGACCACGTCTG
11129 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
66 GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
11163 TATCGCTTCG
Statistics
Matches: 184, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 184 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (99 bp):
ATTTCGTGTAAGACCCTGTCTGGGATAGAGGCATCAATATTGAATTACATGTAAGACCACGTCTG
GGACGTTGGCATTGTACTTGTTTATGAGTATCTG
Found at i:19338 original size:32 final size:33
Alignment explanation
Indices: 19302--19363 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
19292 AGCTTTCGGC
*
19302 TAGCCGGAATTAAT-CTCGCCAATGCTCGGGCT
1 TAGCCGGAATTAATCCTCGCAAATGCTCGGGCT
*
19334 TAGCCGGAATTGATCCTCGCAAATGCTCGG
1 TAGCCGGAATTAATCCTCGCAAATGCTCGG
19364 ATTATTCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (33 bp):
TAGCCGGAATTAATCCTCGCAAATGCTCGGGCT
Done.