Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1261
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: 125843
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
File 2 of 2
Found at i:122700 original size:16 final size:15
Alignment explanation
Indices: 122679--122743 Score: 62
Period size: 15 Copynumber: 4.2 Consensus size: 15
122669 ATATTAAATA
*
122679 ATTAAATATATATTTT
1 ATTAAATAT-TATTAT
122695 ATTAAATATTATTAT
1 ATTAAATATTATTAT
*
122710 ATTTAATATTCATTTACT
1 ATTAAATATT-A-TTA-T
122728 ATTAAA-ATTATT-T
1 ATTAAATATTATTAT
122741 ATT
1 ATT
122744 CATTGTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 4 0.09
15 16 0.37
16 11 0.26
17 6 0.14
18 6 0.14
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTAAATATTATTAT
Found at i:122712 original size:39 final size:39
Alignment explanation
Indices: 122632--122706 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 39
122622 TTTTATAAAA
* *
122632 ATTAAATATTTAAAATCTAATATTTATATTAAAAATTAT
1 ATTAAATAATTAAAATATAATATTTATATTAAAAATTAT
*
122671 ATTAAATAATT-AAATAT-ATATTT-TATTAAATATTAT
1 ATTAAATAATTAAAATATAATATTTATATTAAAAATTAT
122707 TATATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 12 0.36
37 6 0.18
38 5 0.15
39 10 0.30
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (39 bp):
ATTAAATAATTAAAATATAATATTTATATTAAAAATTAT
Found at i:123572 original size:16 final size:17
Alignment explanation
Indices: 123538--123586 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
123528 TAACTAAATA
*
123538 ATTAAATGTA-TATTTAT
1 ATTAAATATATTA-TTAT
123555 ATTAAATAT-TTATTAT
1 ATTAAATATATTATTAT
*
123571 ATTTAATATATTATTA
1 ATTAAATATATTATTA
123587 AAATTAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTAAATATATTATTAT
Found at i:123586 original size:17 final size:16
Alignment explanation
Indices: 123551--123586 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
123541 AAATGTATAT
123551 TTATATTAAATATTTA
1 TTATATTAAATATTTA
*
123567 TTATATTTAATATATTA
1 TTATATTAAATAT-TTA
123584 TTA
1 TTA
123587 AAATTAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTAAATATTTA
Found at i:125065 original size:25 final size:27
Alignment explanation
Indices: 125010--125080 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
125000 AAAAATTTAA
* * *
125010 AATTAATTTTTTTATTTTTATTGATTC
1 AATTAAATTTTTTATTTTTATTAAGTC
125037 AATTAAATTTTTTATTTTTA-TAAGT-
1 AATTAAATTTTTTATTTTTATTAAGTC
*
125062 AATTTAATTTTTTATTTTT
1 AATTAAATTTTTTATTTTT
125081 TTTTTTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 18 0.45
26 3 0.08
27 19 0.47
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (27 bp):
AATTAAATTTTTTATTTTTATTAAGTC
Found at i:125694 original size:26 final size:30
Alignment explanation
Indices: 125665--125735 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
125655 TAAAAATATT
125665 ATTTTA-TTTTTAT-TTA-AATT-AATTAA
1 ATTTTATTTTTTATATTATAATTAAATTAA
*
125691 ATTTATATTTTTTATATTATTATTAAATTAA
1 ATTT-TATTTTTTATATTATAATTAAATTAA
125722 ATTTTTATATTTTT
1 A-TTTTAT-TTTTT
125736 TTCTATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 4 0.11
27 2 0.05
28 7 0.19
29 3 0.08
30 3 0.08
31 10 0.27
32 8 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
ATTTTATTTTTTATATTATAATTAAATTAA
Found at i:125717 original size:35 final size:32
Alignment explanation
Indices: 125660--125736 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 32
125650 ATATATAAAA
125660 ATATTATTTTATTTTTATTTAAATT-AATTAAATTT
1 ATATT-TTTTATTTTTATTTAAATTAAATT---TTT
125695 ATATTTTTTATATTATTA-TTAAATTAAATTTTT
1 ATATTTTTTAT-TT-TTATTTAAATTAAATTTTT
125728 ATATTTTTT
1 ATATTTTTT
125737 TCTATGAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
33 12 0.31
34 6 0.15
35 14 0.36
36 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
ATATTTTTTATTTTTATTTAAATTAAATTTTT
Done.