Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3398
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: 11308
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Found at i:4471 original size:47 final size:47
Alignment explanation
Indices: 4405--4877 Score: 786
Period size: 47 Copynumber: 10.1 Consensus size: 47
4395 GAAATGATAG
4405 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
4452 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
4499 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
4546 TAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
**
4593 TAAGGCCTAATACCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
4640 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
4687 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
4734 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
4781 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
4827 TAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
4874 TAAG
1 TAAG
4878 TCCCGAAGGG
Statistics
Matches: 404, Mismatches: 21, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 0.10
47 363 0.90
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:9270 original size:38 final size:39
Alignment explanation
Indices: 9207--9518 Score: 363
Period size: 39 Copynumber: 8.0 Consensus size: 39
9197 GCAAGACACT
9207 GAAATGTATCC-GGCTAAAGTCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
9245 GAAATGTATCCGGGCTAAAGT-CCGCAGGCTTCGTGCT-
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
*
9282 GAAATATATCCGGGCTAAAGTCCCGCAGGCTTTTGTGTGGCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGC-----T-T--CGTGCTG
* *
9329 GAAATATTATCCGGG---AAGTCCCGCA-GCTTCGTGCTA
1 GAAAT-GTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* * *
9365 GAAATATATCCAGGCCAAA-TCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* *
9403 GAAATGTATCTGGGCCAAAGTCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* *
9442 GAAATGTATCCGGGCCAAAGTCTCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* * *
9481 GAAATGTATCCGAGTTAAAGT-CCGCAGGCTTTGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
9519 ATAATAATTT
Statistics
Matches: 241, Mismatches: 16, Indels: 34
0.83 0.05 0.12
Matches are distributed among these distances:
35 7 0.03
36 11 0.05
37 27 0.11
38 79 0.33
39 84 0.35
43 1 0.00
44 3 0.01
45 10 0.04
46 6 0.02
47 5 0.02
48 8 0.03
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
Found at i:9388 original size:82 final size:82
Alignment explanation
Indices: 9238--9524 Score: 252
Period size: 77 Copynumber: 3.6 Consensus size: 82
9228 CCGCAGGCTT
* *
9238 CGTGCTGGAAATGTATCCGGGCTAAAGTCCGCAGGCTTCGTGCTGAAATATATCCGGGCTAAAGT
1 CGTGCTGGAAATGTATCCGGG--AAAGTCCGCAGGCTTCGTGCTGAAATATATCCAGGCCAAAGT
9303 CCCGCAGGCTTTTGTGTGG
64 CCCGCAGGCTTTTGTGTGG
*
9322 CGTGCTGGAAATATTATCCGGG-AAGTCCCGCA-GCTTCGTGCTAGAAATATATCCAGGCCAAA-
1 CGTGCTGGAAAT-GTATCCGGGAAAGT-CCGCAGGCTTCGTGCT-GAAATATATCCAGGCCAAAG
9384 TCCCGCAGGC-----T-T--
63 TCCCGCAGGCTTTTGTGTGG
* * *
9396 CGTGCTGGAAATGTATCTGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAA
1 CGTGCTGGAAATGTATCCGGG--AAAGT-CCGCAGGCTTCGTGCT-GAAATATATCCAGGCCAAA
*
9461 GTCTCGCAGGC-----T-T--
62 GTCCCGCAGGCTTTTGTGTGG
* *
9474 CGTGCTGGAAATGTATCCGAGTTAAAGTCCGCAGGCTTTGTGCTGATAATA
1 CGTGCTGGAAATGTATCCG-G-GAAAGTCCGCAGGCTTCGTGCTGA-AATA
9525 ATTTCGGGTT
Statistics
Matches: 179, Mismatches: 13, Indels: 29
0.81 0.06 0.13
Matches are distributed among these distances:
73 7 0.04
74 12 0.07
76 13 0.07
77 46 0.26
78 34 0.19
79 1 0.01
82 24 0.13
83 22 0.12
84 12 0.07
85 8 0.04
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (82 bp):
CGTGCTGGAAATGTATCCGGGAAAGTCCGCAGGCTTCGTGCTGAAATATATCCAGGCCAAAGTCC
CGCAGGCTTTTGTGTGG
Done.