Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3776
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: 10217
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Found at i:1720 original size:28 final size:28
Alignment explanation
Indices: 1680--1828 Score: 235
Period size: 28 Copynumber: 5.3 Consensus size: 28
1670 TTAAGTCCGT
* *
1680 ACACTCAGTGCTATGTAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
1708 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
1736 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
1764 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
* * * *
1792 ACACTTAGTGCTGTACAATTTAAACCCGC
1 ACACTTAGTGCTATATAA-TCAAACTCGC
1821 ACACTTAG
1 ACACTTAG
1829 CGCCAATCTC
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
28 98 0.86
29 16 0.14
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (28 bp):
ACACTTAGTGCTATATAATCAAACTCGC
Found at i:9044 original size:28 final size:28
Alignment explanation
Indices: 8985--9069 Score: 147
Period size: 28 Copynumber: 3.1 Consensus size: 28
8975 ATATTAAGTC
*
8985 CGCACACTCAGTGCTAT-TAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
9011 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
9039 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
9067 CGC
1 CGC
9070 TTAGTGCTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
26 16 0.29
27 5 0.09
28 35 0.62
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.