Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01949.F2

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: 3678
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:1837 original size:27 final size:27

Alignment explanation


    Indices: 1795--1871  Score: 109
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       1785 AATTTAAGAT

                                   * * 
       1795 CAAGCCATGGTGATCAACAACCTTTGC
          1 CAAGCCATGGTGATCAACAACCTGTAC

             * *                *      
       1822 CGATCCATGGTGATCAACAATCTGTAC
          1 CAAGCCATGGTGATCAACAACCTGTAC

                                   
       1849 CAAGCCATGGTGATCAACAACCT
          1 CAAGCCATGGTGATCAACAACCT

       1872 ATGTCAAACC


Statistics
Matches: 42,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   42  1.00

ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22


Consensus pattern (27 bp):   
CAAGCCATGGTGATCAACAACCTGTAC

Found at i:1883 original size:27 final size:27

Alignment explanation


    Indices: 1795--1883  Score: 106
    Period size: 27  Copynumber: 3.3  Consensus size: 27

       1785 AATTTAAGAT

                                   *   
       1795 CAAGCCATGGTGATCAACAACCTTTGC
          1 CAAGCCATGGTGATCAACAACCTATGC

             * *                *  * * 
       1822 CGATCCATGGTGATCAACAATCTGTAC
          1 CAAGCCATGGTGATCAACAACCTATGC

                                      *
       1849 CAAGCCATGGTGATCAACAACCTATGT
          1 CAAGCCATGGTGATCAACAACCTATGC

               *    
       1876 CAAACCAT
          1 CAAGCCAT

       1884 ATTACCAACT


Statistics
Matches: 50,  Mismatches: 12, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  27   50  1.00

ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22


Consensus pattern (27 bp):   
CAAGCCATGGTGATCAACAACCTATGC

Found at i:1996 original size:171 final size:171

Alignment explanation


    Indices: 1711--2053  Score: 614
    Period size: 171  Copynumber: 2.0  Consensus size: 171

       1701 CCTGTGGCTT

                             *                                               
       1711 ATATTACCAACTATGATTCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG
          1 ATATTACCAACTATGATCCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG

                                          *                                  
       1776 AAGAGACCTAATTTAAGATCAAGCCATGGTGATCAACAACCTTTGCCGATCCATGGTGATCAACA
         66 AAGAGACCTAATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCCGATCCATGGTGATCAACA

                                                     
       1841 ATCTGTACCAAGCCATGGTGATCAACAACCTATGTCAAACC
        131 ATCTGTACCAAGCCATGGTGATCAACAACCTATGTCAAACC

                                                                  *          
       1882 ATATTACCAACTATGATCCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACTACCTAGGAGG
          1 ATATTACCAACTATGATCCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG

                     **                             *         *              
       1947 AAGAGACCTCGTTTAAGATCAAGCCATGGTCATCAACAACTTTTGCCGATTCATGGTGATCAACA
         66 AAGAGACCTAATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCCGATCCATGGTGATCAACA

                    *                                
       2012 ATCTGTACTAAGCCATGGTGATCAACAACCTATGTCAAACC
        131 ATCTGTACCAAGCCATGGTGATCAACAACCTATGTCAAACC

             
       2053 A
          1 A

       2054 CAGTGATCAA


Statistics
Matches: 164,  Mismatches: 8, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 171  164  1.00

ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22


Consensus pattern (171 bp):   
ATATTACCAACTATGATCCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG
AAGAGACCTAATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCCGATCCATGGTGATCAACA
ATCTGTACCAAGCCATGGTGATCAACAACCTATGTCAAACC

Found at i:2028 original size:27 final size:26

Alignment explanation


    Indices: 1998--2093  Score: 113
    Period size: 27  Copynumber: 3.6  Consensus size: 26

       1988 TTTGCCGATT

                                       
       1998 CATGGTGATCAACAATCTGTACTAAGC
          1 CATGGTGATCAACAATCTGTAC-AAGC

                              *       * 
       2025 CATGGTGATCAACAACCTATGT-CAAAC
          1 CATGGTGATCAACAA--TCTGTACAAGC

              **                       
       2052 CACAGTGATCAACAATCTGTACCAAGC
          1 CATGGTGATCAACAATCTGTA-CAAGC

                           
       2079 CATGGTGATCAACAA
          1 CATGGTGATCAACAA

       2094 CCTGGACCAC


Statistics
Matches: 57,  Mismatches: 8, Indels: 8
        0.78            0.11        0.11

Matches are distributed among these distances:
  25    4  0.07
  27   48  0.84
  28    1  0.02
  29    4  0.07

ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22


Consensus pattern (26 bp):   
CATGGTGATCAACAATCTGTACAAGC

Done.