Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2248

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: 16713
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31


Found at i:5064 original size:40 final size:40

Alignment explanation


    Indices: 4929--5113  Score: 299
    Period size: 40  Copynumber: 4.7  Consensus size: 40

       4919 TATTCGGATG

                                            *   *   
       4929 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT

                *                                    
       4969 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTA-T
          1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT

                                                    
       5007 AT--CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT

                                                    
       5045 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT

                                         
       5085 ATAACCGGGCTAAGTCCCGAAGGCATTTG
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTG

       5114 AGCAAGTAGC


Statistics
Matches: 136,  Mismatches: 3, Indels: 12
        0.90            0.02        0.08

Matches are distributed among these distances:
  36   10  0.07
  37   23  0.17
  38    5  0.04
  39   22  0.16
  40   76  0.56

ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25


Consensus pattern (40 bp):   
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT

Found at i:5127 original size:40 final size:40

Alignment explanation


    Indices: 4929--5146  Score: 265
    Period size: 40  Copynumber: 5.6  Consensus size: 40

       4919 TATTCGGATG

                                            *        
       4929 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACT
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAG-CT

                *                                    
       4969 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGT---T
          1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCT

               *                                     
       5005 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCT

                                                     
       5045 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCT

                                         *  *       
       5085 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGCT
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCT

               *         * *       
       5125 ATATCC-GGCTAAATTCCGAAGG
          1 ATAACCGGGCTAAGTCCCGAAGG

       5147 TACTTGGTTT


Statistics
Matches: 163,  Mismatches: 8, Indels: 15
        0.88            0.04        0.08

Matches are distributed among these distances:
  36   13  0.08
  37   21  0.13
  38    1  0.01
  39   37  0.23
  40   91  0.56

ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24


Consensus pattern (40 bp):   
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCT
Done.