Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3013

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: 20153
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33


Found at i:4932 original size:19 final size:22

Alignment explanation


    Indices: 4883--4933  Score: 56
    Period size: 18  Copynumber: 2.5  Consensus size: 22

       4873 ATTAAATAAA

                                   
       4883 TATTAGTTTATAATATTTAATTT
          1 TATTA-TTTATAATATTTAATTT

            *                     
       4906 AATT-TTTA-AATA-TT-ATTT
          1 TATTATTTATAATATTTAATTT

                      
       4924 TATTATTTAT
          1 TATTATTTAT

       4934 TTAGCATTTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 7
        0.73            0.06        0.21

Matches are distributed among these distances:
  18    7  0.29
  19    6  0.25
  20    4  0.17
  21    4  0.17
  23    3  0.12

ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63


Consensus pattern (22 bp):   
TATTATTTATAATATTTAATTT

Found at i:11623 original size:16 final size:16

Alignment explanation


    Indices: 11594--11632  Score: 55
    Period size: 16  Copynumber: 2.5  Consensus size: 16

      11584 ATTCATTTGA

                            
      11594 CATT-CATCATTCATT
          1 CATTGCATCATTCATT

                             
      11609 CA-TGCATCAATTCATT
          1 CATTGCATC-ATTCATT

                    
      11625 CATTGCAT
          1 CATTGCAT

      11633 TATCCCATAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  14    1  0.05
  15    6  0.29
  16    9  0.43
  17    5  0.24

ACGTcount: A:0.28, C:0.26, G:0.05, T:0.41


Consensus pattern (16 bp):   
CATTGCATCATTCATT

Found at i:12788 original size:104 final size:107

Alignment explanation


    Indices: 12607--12821  Score: 384
    Period size: 104  Copynumber: 2.0  Consensus size: 107

      12597 AAATCTTTGT

                                                                             
      12607 ATTCGCGGAGTAAAGTGATCAAATATGCCTGGTACTTTTCTGAAATAGAAGTCCCAATCTTCACT
          1 ATTCGCGGAGTAAAGTGATCAAATATGCCTGGTACTTTTCTGAAATAGAAGTCCCAATCTTCACT

                                                      
      12672 CTTGTTTCCTCTCTCAGTGCCCAAATTTA-TTG-TTCTACAG
         66 CTTGTTTCCTCTCTCAGTGCCCAAATTTATTTGTTTCTACAG

                                                                             
      12712 ATTCGCGGAGTAAAGTGATCAAACTATG-CTGGTAC-TTTCTGAAATAGAAGTCCCAATCTTCAC
          1 ATTCGCGGAGTAAAGTGATCAAA-TATGCCTGGTACTTTTCTGAAATAGAAGTCCCAATCTTCAC

             *                                         
      12775 TTTTGTTTCCTCTCTCAGTGCCCAAATTTATTTGTTTCTACAG
         65 TCTTGTTTCCTCTCTCAGTGCCCAAATTTATTTGTTTCTACAG

                
      12818 ATTC
          1 ATTC

      12822 TTCATGAGGC


Statistics
Matches: 106,  Mismatches: 1, Indels: 5
        0.95            0.01        0.04

Matches are distributed among these distances:
 104   57  0.54
 105   33  0.31
 106   16  0.15

ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36


Consensus pattern (107 bp):   
ATTCGCGGAGTAAAGTGATCAAATATGCCTGGTACTTTTCTGAAATAGAAGTCCCAATCTTCACT
CTTGTTTCCTCTCTCAGTGCCCAAATTTATTTGTTTCTACAG
Done.