Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold363
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: 552799
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
File 4 of 4
Found at i:551230 original size:4 final size:4
Alignment explanation
Indices: 551221--551255 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
551211 TCCATTAAAA
*
551221 TAAT TAAT TAAG TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
551256 AAATGCAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (4 bp):
TAAT
Found at i:551766 original size:27 final size:27
Alignment explanation
Indices: 551731--551782 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
551721 TTTAATTATC
551731 ATTTTAAAATAGTATAT-ATTTATATAA
1 ATTTTAAAATAGTA-ATCATTTATATAA
*
551758 ATTTTAAAATATTAATCATTTATAT
1 ATTTTAAAATAGTAATCATTTATAT
551783 TTTATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTTTAAAATAGTAATCATTTATATAA
Found at i:551869 original size:19 final size:18
Alignment explanation
Indices: 551798--551870 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
551788 AAATTTTAAG
551798 ATATTTTATATTTATACTGT
1 ATATTTTATATTTATA-T-T
* *
551818 A-ATTATATTATTTTATATA
1 ATATTTTA-TA-TTTATATT
551837 ATATTTTATAATTTATATT
1 ATATTTTAT-ATTTATATT
551856 ATATTTTAATATTTA
1 ATATTTT-ATATTTA
551871 GCACAAGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
19 26 0.59
20 12 0.27
21 6 0.14
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (18 bp):
ATATTTTATATTTATATT
Found at i:552697 original size:15 final size:15
Alignment explanation
Indices: 552677--552706 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
552667 ATTTTTTTTA
552677 ATATTTTTTAAATTT
1 ATATTTTTTAAATTT
*
552692 ATATTTTTTATATTT
1 ATATTTTTTAAATTT
552707 TATAATCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATATTTTTTAAATTT
Found at i:552701 original size:9 final size:9
Alignment explanation
Indices: 552654--552707 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
552644 AAATATATTA
552654 TTTTTAT-T
1 TTTTTATAT
*
552662 TTTTTATTT
1 TTTTTATAT
552671 TTTTTAATAT
1 TTTTT-ATAT
552681 TTTTTA-A-
1 TTTTTATAT
*
552688 -ATTTATAT
1 TTTTTATAT
552696 TTTTTATAT
1 TTTTTATAT
552705 TTT
1 TTT
552708 ATAATCTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
6 4 0.11
7 1 0.03
8 8 0.21
9 17 0.45
10 8 0.21
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTATAT
Found at i:552717 original size:25 final size:25
Alignment explanation
Indices: 552664--552711 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
552654 TTTTTATTTT
* *
552664 TTTATTTTTTTTAATATTTTTTAAA
1 TTTATATTTTTTAATATTTTATAAA
552689 TTTATATTTTTT-ATATTTTATAA
1 TTTATATTTTTTAATATTTTATAA
552712 TCTTTAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTATATTTTTTAATATTTTATAAA
Done.