Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00632.N1

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: 3407
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32


Found at i:291 original size:19 final size:18

Alignment explanation


    Indices: 267--312  Score: 74
    Period size: 19  Copynumber: 2.5  Consensus size: 18

        257 TATTTTGTTA

                               
        267 TTTATTTTTATTTCATCTT
          1 TTTATTTTTATTTCATC-T

                    *         
        286 TTTATTTTCATTTCATCT
          1 TTTATTTTTATTTCATCT

                     
        304 TTTATTTTT
          1 TTTATTTTT

        313 TACTTTTTAC


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  18    9  0.36
  19   16  0.64

ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74


Consensus pattern (18 bp):   
TTTATTTTTATTTCATCT

Found at i:594 original size:48 final size:48

Alignment explanation


    Indices: 523--670  Score: 235
    Period size: 48  Copynumber: 3.1  Consensus size: 48

        513 ACAGCCATCA

                          *                             *   
        523 GCCATTGTATGAATACCATTATCAAATTGATGTGTATTGTGTATGTCT
          1 GCCATTGTATGAATGCCATTATCAAATTGATGTGTATTGTGTATATCT

                                           *                
        571 GCCATTGTATGAATGCCATTATCAAATTGATTTGTATTGTGTATATCT
          1 GCCATTGTATGAATGCCATTATCAAATTGATGTGTATTGTGTATATCT

                                      *      *    *         
        619 GCCATTGTATGAATG-CATTATCAAACTGATGTTTATTTTGTATATCT
          1 GCCATTGTATGAATGCCATTATCAAATTGATGTGTATTGTGTATATCT

                 
        666 GCCAT
          1 GCCAT

        671 GATGTTTATT


Statistics
Matches: 93,  Mismatches: 7, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  47   33  0.35
  48   60  0.65

ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43


Consensus pattern (48 bp):   
GCCATTGTATGAATGCCATTATCAAATTGATGTGTATTGTGTATATCT

Found at i:3010 original size:21 final size:21

Alignment explanation


    Indices: 2980--3033  Score: 72
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       2970 CTCAACAAGG

                         *       
       2980 TGCCCCAACTCAGTTACCTAT
          1 TGCCCCAACTCAGATACCTAT

                 *              *
       3001 TGCCCTAACTCAGATACCTAC
          1 TGCCCCAACTCAGATACCTAT

             *          
       3022 TACCCCAACTCA
          1 TGCCCCAACTCA

       3034 TCAAGAAACT


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.28, C:0.41, G:0.07, T:0.24


Consensus pattern (21 bp):   
TGCCCCAACTCAGATACCTAT
Done.