Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1382
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: 16671
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Found at i:4391 original size:1 final size:1
Alignment explanation
Indices: 4385--4413 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
4375 ATTCTGCTCC
4385 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4414 ATTACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8653 original size:19 final size:20
Alignment explanation
Indices: 8615--8652 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
8605 GATTACTACC
8615 CTTCCTCTCTTTTTCTTTTT
1 CTTCCTCTCTTTTTCTTTTT
8635 CTTCC-CTCTTTTT-TTTTT
1 CTTCCTCTCTTTTTCTTTTT
8653 TAAATCAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
CTTCCTCTCTTTTTCTTTTT
Found at i:14542 original size:1 final size:1
Alignment explanation
Indices: 14536--14748 Score: 210
Period size: 1 Copynumber: 213.0 Consensus size: 1
14526 TTGTTTTATA
* *** *
14536 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTAAATTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * * * * * *
14601 TTTTTTTTTTTTTTTGGTTGTTATTTTTTTTTATTTTTTTTTTTTTTTTTTTTATATTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * **
14666 GTTTTCTTTGTTTATTTTTTTTTTTTTTTATTTTATTTTTTTTTTTTTTTTATTTTTATCATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
14731 TTTTTTATTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTT
14749 CAGCTTTCTC
Statistics
Matches: 171, Mismatches: 41, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 171 1.00
ACGTcount: A:0.07, C:0.01, G:0.03, T:0.89
Consensus pattern (1 bp):
T
Found at i:14694 original size:100 final size:102
Alignment explanation
Indices: 14529--14748 Score: 279
Period size: 100 Copynumber: 2.2 Consensus size: 102
14519 TTTATGTTTG
* * * * *
14529 TTTTATATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTAAATTTTTTTTT
1 TTTTTTATTTTTTTTTTTTTTTTTTTTTTTGTTTTTTGTTTTCTTTGTTTATTAAATTTTTTTTT
*
14594 T-TGTTT-TTTTTTTTTTTTTTTTGGTTGT-T-A-TTT
66 TAT-TTTATTTTTTTTTTTTTTTTAGTTGTATCATTTT
***
14627 TTTTTTATTTTTTTTTTTTTTTTTTTTATATTGTTTTTTGTTTTCTTTGTTTATTTTTTTTTTTT
1 TTTTTTATTTTTTTTTTTTTTTTTTTT-T-TTGTTTTTTGTTTTCTTTGTTTATTAAATTTTTTT
* *
14692 TTTATTTTATTTTTTTTTTTTTTTTATTTTTATCATTTT
64 TTTATTTTATTTTTTTTTTTTTTTTAGTTGTATCATTTT
14731 TTTTTTATTTTTTTTTTT
1 TTTTTTATTTTTTTTTTT
14749 CAGCTTTCTC
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
98 26 0.25
99 1 0.01
100 34 0.33
101 20 0.19
102 1 0.01
103 1 0.01
104 21 0.20
ACGTcount: A:0.08, C:0.01, G:0.03, T:0.88
Consensus pattern (102 bp):
TTTTTTATTTTTTTTTTTTTTTTTTTTTTTGTTTTTTGTTTTCTTTGTTTATTAAATTTTTTTTT
TATTTTATTTTTTTTTTTTTTTTAGTTGTATCATTTT
Done.