Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g01644.P2

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: 19962
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31


Found at i:4859 original size:21 final size:21

Alignment explanation


    Indices: 4833--4873  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4823 AGACGAGCGA

                   * *           
       4833 TACTCCACAGCAGGTGGAGTG
          1 TACTCCAAAACAGGTGGAGTG

                                
       4854 TACTCCAAAACAGGTGGAGT
          1 TACTCCAAAACAGGTGGAGT

       4874 TTGAGCAGAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20


Consensus pattern (21 bp):   
TACTCCAAAACAGGTGGAGTG

Found at i:8080 original size:25 final size:25

Alignment explanation


    Indices: 8046--8096  Score: 75
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       8036 TTCCTTATAA

                        *    **      
       8046 ACTTTAAATTAGGAATTCTATTAGG
          1 ACTTTAAATTAGAAATTAGATTAGG

                                     
       8071 ACTTTAAATTAGAAATTAGATTAGG
          1 ACTTTAAATTAGAAATTAGATTAGG

             
       8096 A
          1 A

       8097 TTTTTCTTTG


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  25   23  1.00

ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37


Consensus pattern (25 bp):   
ACTTTAAATTAGAAATTAGATTAGG

Found at i:12747 original size:25 final size:25

Alignment explanation


    Indices: 12713--12761  Score: 80
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      12703 CCTTATAAAT

                           **        
      12713 TTTAAATTAGGAATTCTATTAGGAC
          1 TTTAAATTAGGAATTAGATTAGGAC

                                    
      12738 TTTAAATTAGGAATTAGATTAGGA
          1 TTTAAATTAGGAATTAGATTAGGA

      12762 TTTTCCTTTG


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39


Consensus pattern (25 bp):   
TTTAAATTAGGAATTAGATTAGGAC

Found at i:12760 original size:12 final size:12

Alignment explanation


    Indices: 12714--12761  Score: 51
    Period size: 12  Copynumber: 3.9  Consensus size: 12

      12704 CTTATAAATT

                        
      12714 TTAAATTAGGAA
          1 TTAAATTAGGAA

              **        *
      12726 TTCTATTAGGACT
          1 TTAAATTAGGA-A

                        
      12739 TTAAATTAGGAA
          1 TTAAATTAGGAA

               *       
      12751 TTAGATTAGGA
          1 TTAAATTAGGA

      12762 TTTTCCTTTG


Statistics
Matches: 28,  Mismatches: 7, Indels: 2
        0.76            0.19        0.05

Matches are distributed among these distances:
  12   19  0.68
  13    9  0.32

ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38


Consensus pattern (12 bp):   
TTAAATTAGGAA

Found at i:19036 original size:18 final size:18

Alignment explanation


    Indices: 18999--19072  Score: 87
    Period size: 18  Copynumber: 4.1  Consensus size: 18

      18989 CAATCCTAAC

                      * *  *  
      18999 TACTGTATACGTGAACAG
          1 TACTGTATACATAAATAG

                              
      19017 TACTGTATACATAAATAG
          1 TACTGTATACATAAATAG

               *               
      19035 TACCGTATACATAAAATAG
          1 TACTGTATACAT-AAATAG

                               
      19054 TA-TCGTATACATAAATAG
          1 TACT-GTATACATAAATAG

             
      19072 T
          1 T

      19073 GTCGTAAATG


Statistics
Matches: 49,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  18   33  0.67
  19   16  0.33

ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31


Consensus pattern (18 bp):   
TACTGTATACATAAATAG

Found at i:19053 original size:19 final size:18

Alignment explanation


    Indices: 19015--19072  Score: 89
    Period size: 18  Copynumber: 3.2  Consensus size: 18

      19005 ATACGTGAAC

                 *            
      19015 AGTACTGTATACATAAAT
          1 AGTACCGTATACATAAAT

                               
      19033 AGTACCGTATACATAAAAT
          1 AGTACCGTATACAT-AAAT

                *             
      19052 AGTATCGTATACATAAAT
          1 AGTACCGTATACATAAAT

               
      19070 AGT
          1 AGT

      19073 GTCGTAAATG


Statistics
Matches: 37,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   20  0.54
  19   17  0.46

ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31


Consensus pattern (18 bp):   
AGTACCGTATACATAAAT

Found at i:19077 original size:18 final size:18

Alignment explanation


    Indices: 19021--19078  Score: 89
    Period size: 18  Copynumber: 3.2  Consensus size: 18

      19011 GAACAGTACT

                            * 
      19021 GTATACATAAATAGTACC
          1 GTATACATAAATAGTATC

                               
      19039 GTATACATAAAATAGTATC
          1 GTATACAT-AAATAGTATC

                           *  
      19058 GTATACATAAATAGTGTC
          1 GTATACATAAATAGTATC

               
      19076 GTA
          1 GTA

      19079 AATGGTCGTA


Statistics
Matches: 37,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  18   20  0.54
  19   17  0.46

ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31


Consensus pattern (18 bp):   
GTATACATAAATAGTATC
Done.