Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2290
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: 30751
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:19079 original size:19 final size:17
Alignment explanation
Indices: 19057--19119 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 17
19047 ATTATCTTCT
19057 TCATTATTTTAATGTATTA
1 TCATTATTTT-AT-TATTA
19076 TCATTTATTATTATTATTA
1 TCA-TTATT-TTATTATTA
*
19095 TTATTATTTCTATTATTA
1 TCATTATTT-TATTATTA
*
19113 TTATTAT
1 TCATTAT
19120 GTACATTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 1 0.03
18 20 0.50
19 10 0.25
20 7 0.17
21 2 0.05
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
TCATTATTTTATTATTA
Found at i:19088 original size:3 final size:3
Alignment explanation
Indices: 19080--19150 Score: 65
Period size: 3 Copynumber: 23.3 Consensus size: 3
19070 GTATTATCAT
*
19080 TTA TTA TTA TTA TTA TTA TTA TT- TCTA TTA TTA TTA TTA TGTA -CA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA
* * *
19125 TTA CTG TTA CTTA TCA TTA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA T
19151 GTGATAGCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 2 0.04
3 47 0.85
4 6 0.11
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Done.