Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3262
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: 23215
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:17082 original size:17 final size:17
Alignment explanation
Indices: 17051--17084 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17041 CATGGTAAAT
* *
17051 AATAAAAAGTCAACAAA
1 AATAAAAAATAAACAAA
17068 AATAAAAAATAAACAAA
1 AATAAAAAATAAACAAA
17085 TAAGAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (17 bp):
AATAAAAAATAAACAAA
Found at i:19228 original size:87 final size:88
Alignment explanation
Indices: 19123--19492 Score: 210
Period size: 87 Copynumber: 4.3 Consensus size: 88
19113 GACCTACTCT
* * * * * *
19123 GCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCACTCCACTGTAACTTCAGGGAGATA
1 GCTGTAATCTCAGGGAGATAAGATCTC-TGACTTCAATCCACTCCACTGTAACCTCAGGGAGATA
* *
19187 GGA-T-AGTGTCTTCGATCTGCTCC
65 AGACTAAAT-TCTTCGATCTGCTCC
* **
19210 GCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAA
1 GCTGTAATCTCAGGGAGATAAGATCTCTGACTTCAATCCACTCCACTGTAACCTCAGGGAGATAA
* * *
19275 GATCTAAAATTCTTTGGTCTGTTCC
66 GA-CT-AAATTCTTCGATCTGCTCC
* * ** * * *
19300 ACTGTAATCTCAGGGAGATAAGA-C-CTGA-TGT-GATCTTCTCTACTGTAACTTCAGAGAGATA
1 GCTGTAATCTCAGGGAGATAAGATCTCTGACT-TCAATCCACTCCACTGTAACCTCAGGGAGATA
* ** *
19361 AG-----ATCCTTTAATCCGCTCC
65 AGACTAAATTCTTCGATCTGCTCC
** * * ** ** * *
19380 ATTGTAATCTCAAGGAGATAGGAT-TACT-ATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGAT
1 GCTGTAATCTCAGGGAGATAAGATCT-CTGA-CTTCAATCCACTCCACTGTAACCTCAGGGAGAT
* * *
19443 AAGATCTGAAATTCTTTGGTCTGTTCC
64 AAGA-CT-AAATTCTTCGATCTGCTCC
*
19470 ACTGTAATCTCAGGGAGATAAGA
1 GCTGTAATCTCAGGGAGATAAGA
19493 CCTGTATAAT
Statistics
Matches: 221, Mismatches: 43, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
80 32 0.14
81 1 0.00
82 3 0.01
83 27 0.12
87 83 0.38
88 5 0.02
89 2 0.01
90 66 0.30
91 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (88 bp):
GCTGTAATCTCAGGGAGATAAGATCTCTGACTTCAATCCACTCCACTGTAACCTCAGGGAGATAA
GACTAAATTCTTCGATCTGCTCC
Found at i:19315 original size:46 final size:43
Alignment explanation
Indices: 19163--19492 Score: 241
Period size: 44 Copynumber: 7.6 Consensus size: 43
19153 TTTTAATCCA
* * * *
19163 CTCCACTGTAA-CTTCAGGGAGATAGGATAGT-GTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGAT-CTAATCTTTGATCTG
* * **
19206 CTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTAAT--CTTTGATCTG
* *
19250 CTCCACTGTAACCTCAGGGAGATAAGATCTAAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT--AA-TCTTTGATCTG
* * * * *
19296 TTCCACTGTAATCTCAGGGAGATAAGACCTGA--TGTGATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTAATCTTTGATCTG
* * * *
19337 CTCTACTGTAA-CTTCAGAGAGATAAGATC----CTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTAATCTTTGATCTG
* * *
19376 CTCCATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTA--ATCTTTGATCTG
* *
19420 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT--AA-TCTTTGATCTG
*
19466 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
19493 CCTGTATAAT
Statistics
Matches: 227, Mismatches: 40, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
39 26 0.11
40 2 0.01
41 29 0.13
42 2 0.01
43 24 0.11
44 71 0.31
45 2 0.01
46 69 0.30
47 1 0.00
48 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTAATCTTTGATCTG
Done.