Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3532

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: 21665
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31


Found at i:10829 original size:40 final size:40

Alignment explanation


    Indices: 10785--10860  Score: 107
    Period size: 40  Copynumber: 1.9  Consensus size: 40

      10775 AGTGAATATA

                        *                           
      10785 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACAAGT
          1 TCCGGACTAAGACCCGAAGGCATTTGTGCGAGATACAAGT

                 **    *         *              
      10825 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
          1 TCCGGACTAAGACCCGAAGGCATTTGTGCGAGATAC

      10861 TAAATCCGGG


Statistics
Matches: 31,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  40   31  1.00

ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22


Consensus pattern (40 bp):   
TCCGGACTAAGACCCGAAGGCATTTGTGCGAGATACAAGT

Found at i:10869 original size:40 final size:40

Alignment explanation


    Indices: 10798--10882  Score: 127
    Period size: 40  Copynumber: 2.1  Consensus size: 40

      10788 GGACTAAGAT

                                      *             
      10798 CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAGCC
          1 CCGAAGGCATTTGTGCGAGATACAAGATCCGGGTTAAGCC

                    *                              * 
      10838 CCGAAGGCCTTTGTGCGAGATACTAA-ATCCGGGTTAAGTC
          1 CCGAAGGCATTTGTGCGAGATAC-AAGATCCGGGTTAAGCC

                 
      10878 CCGAA
          1 CCGAA

      10883 TGTGACAGCC


Statistics
Matches: 41,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  40   39  0.95
  41    2  0.05

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


Consensus pattern (40 bp):   
CCGAAGGCATTTGTGCGAGATACAAGATCCGGGTTAAGCC

Found at i:13028 original size:40 final size:40

Alignment explanation


    Indices: 12959--13143  Score: 322
    Period size: 40  Copynumber: 4.7  Consensus size: 40

      12949 GCAGCATTGA

                                                    
      12959 ATATATCCGGGCTAA-ACCCGAAGGCAATTATGCGAGTTG
          1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG

                                                    
      12998 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
          1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG

                                                   *
      13038 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAG-TA
          1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG

                                                    
      13077 ATATATCCGGGCTAAGA-CCGAAGGCAATTATGCGAGTTG
          1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG

                *      *                
      13116 ATATGTCCGGGTTAAGACCCGAAGGCAA
          1 ATATATCCGGGCTAAGACCCGAAGGCAA

      13144 ATGTGTTTGC


Statistics
Matches: 139,  Mismatches: 4, Indels: 5
        0.94            0.03        0.03

Matches are distributed among these distances:
  38   19  0.14
  39   49  0.35
  40   71  0.51

ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22


Consensus pattern (40 bp):   
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG

Found at i:13132 original size:78 final size:80

Alignment explanation


    Indices: 12959--13143  Score: 322
    Period size: 78  Copynumber: 2.4  Consensus size: 80

      12949 GCAGCATTGA

                                                   *                         
      12959 ATATATCCGGGCTAA-ACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
          1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCCGAAGG

                           
      13023 CAATTATGCGAGTTG
         66 CAATTATGCGAGTTG

                                                                             
      13038 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAG-TAATATATCCGGGCTAAGA-CCGAAGG
          1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCCGAAGG

                           
      13101 CAATTATGCGAGTTG
         66 CAATTATGCGAGTTG

                *      *                
      13116 ATATGTCCGGGTTAAGACCCGAAGGCAA
          1 ATATATCCGGGCTAAGACCCGAAGGCAA

      13144 ATGTGTTTGC


Statistics
Matches: 102,  Mismatches: 3, Indels: 3
        0.94            0.03        0.03

Matches are distributed among these distances:
  78   48  0.47
  79   33  0.32
  80   21  0.21

ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22


Consensus pattern (80 bp):   
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCCGAAGG
CAATTATGCGAGTTG
Done.