Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03587.F1

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, 835

Length: 1393
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25


Found at i:868 original size:24 final size:24

Alignment explanation


    Indices: 841--930  Score: 81
    Period size: 27  Copynumber: 3.5  Consensus size: 24

        831 CTAACAACAT

                          *         
        841 GGGAGGAATGCCTTACAACAATAG
          1 GGGAGGAATGCCTTCCAACAATAG

                  *     **             
        865 GGGAGGTATGCCAGCCAACAATATGGG
          1 GGGAGGAATGCCTTCCAACAATA---G

                                      *
        892 GGGAGGAATGCCTCCTCCTAACAATAT
          1 GGGAGGAATGCCT--TCC-AACAATAG

                        
        919 GGGAGGAATGCC
          1 GGGAGGAATGCC

        931 GCCGCGGAAC


Statistics
Matches: 52,  Mismatches: 8, Indels: 9
        0.75            0.12        0.13

Matches are distributed among these distances:
  24   19  0.37
  27   24  0.46
  29    2  0.04
  30    7  0.13

ACGTcount: A:0.31, C:0.20, G:0.32, T:0.17


Consensus pattern (24 bp):   
GGGAGGAATGCCTTCCAACAATAG

Found at i:922 original size:27 final size:27

Alignment explanation


    Indices: 892--1098  Score: 234
    Period size: 27  Copynumber: 7.4  Consensus size: 27

        882 ACAATATGGG

                        *           *  
        892 GGGAGGAATGCCTCCTCCTAACAATAT
          1 GGGAGGAATGCCGCCTCCTAACAACAT

                           * **        
        919 GGGAGGAATGCCGCCGCGGAACAACAT
          1 GGGAGGAATGCCGCCTCCTAACAACAT

                                       *  
        946 GGGAGGAGGAATGCCGCCTCCTAACAATAT
          1 --G-GGAGGAATGCCGCCTCCTAACAACAT

                        *  * **        
        976 GGGAGGAATGCCACCGCGGAACAACAT
          1 GGGAGGAATGCCGCCTCCTAACAACAT

                               *       *  
       1003 GGGAGGAGGAATGCCGCCTTCTAACAATAT
          1 --G-GGAGGAATGCCGCCTCCTAACAACAT

                                       
       1033 GGGAGGAATGCCGCCTCCTAACAACAT
          1 GGGAGGAATGCCGCCTCCTAACAACAT

                                       
       1060 GGGAGGAATGCCGCCTCCTAACAACAT
          1 GGGAGGAATGCCGCCTCCTAACAACAT

               *  *     
       1087 GGGTGGGATGCC
          1 GGGAGGAATGCC

       1099 ACCAGGTCCA


Statistics
Matches: 150,  Mismatches: 24, Indels: 12
        0.81            0.13        0.06

Matches are distributed among these distances:
  27  104  0.69
  28    2  0.01
  29    2  0.01
  30   42  0.28

ACGTcount: A:0.29, C:0.25, G:0.31, T:0.15


Consensus pattern (27 bp):   
GGGAGGAATGCCGCCTCCTAACAACAT

Found at i:966 original size:57 final size:57

Alignment explanation


    Indices: 881--1098  Score: 316
    Period size: 57  Copynumber: 3.9  Consensus size: 57

        871 TATGCCAGCC

                 *     *           *                                 
        881 AACAATATGGGGGGAGGAATGCCTCCTCCTAACAATATGGGAGGAATGCCGCCGCGG
          1 AACAACATGGGAGGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCGCCGCGG

                                                              *      
        938 AACAACATGGGAGGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCACCGCGG
          1 AACAACATGGGAGGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCGCCGCGG

                                       *                         * **
        995 AACAACATGGGAGGAGGAATGCCGCCTTCTAACAATATGGGAGGAATGCCGCCTCCT
          1 AACAACATGGGAGGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCGCCGCGG

                                               *     *  *     
       1052 AACAACAT--G-GGAGGAATGCCGCCTCCTAACAACATGGGTGGGATGCC
          1 AACAACATGGGAGGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCC

       1099 ACCAGGTCCA


Statistics
Matches: 148,  Mismatches: 13, Indels: 3
        0.90            0.08        0.02

Matches are distributed among these distances:
  54   34  0.23
  55    1  0.01
  57  113  0.76

ACGTcount: A:0.30, C:0.24, G:0.31, T:0.15


Consensus pattern (57 bp):   
AACAACATGGGAGGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCGCCGCGG

Found at i:984 original size:84 final size:81

Alignment explanation


    Indices: 892--1098  Score: 236
    Period size: 84  Copynumber: 2.5  Consensus size: 81

        882 ACAATATGGG

                        *           *                                        
        892 GGGAGGAATGCCTCCTCCTAACAATATGGGAGGAATGCCGCC-GCGGAACAACATGGGAGGAGGA
          1 GGGAGGAATGCCACCTCCTAACAACATGGGAGGAATGCCGCCTGC-GAACAACAT--G-GGAGGA

                             *  
        956 ATGCCGCCTCCTAACAATAT
         62 ATGCCGCCTCCTAACAACAT

                           * **                           * *     *          
        976 GGGAGGAATGCCACCGCGGAACAACATGGGAGGAGGAATGCCGCCTTCTAACAATATGGGAGGAA
          1 GGGAGGAATGCCACCTCCTAACAACAT--G-GGAGGAATGCCGCCTGCGAACAACATGGGAGGAA

                               
       1041 TGCCGCCTCCTAACAACAT
         63 TGCCGCCTCCTAACAACAT

                        *                 *  *     
       1060 GGGAGGAATGCCGCCTCCTAACAACATGGGTGGGATGCC
          1 GGGAGGAATGCCACCTCCTAACAACATGGGAGGAATGCC

       1099 ACCAGGTCCA


Statistics
Matches: 104,  Mismatches: 15, Indels: 11
        0.80            0.12        0.08

Matches are distributed among these distances:
  81    9  0.09
  82    1  0.01
  84   70  0.67
  85    1  0.01
  86    1  0.01
  87   21  0.20
  88    1  0.01

ACGTcount: A:0.29, C:0.25, G:0.31, T:0.15


Consensus pattern (81 bp):   
GGGAGGAATGCCACCTCCTAACAACATGGGAGGAATGCCGCCTGCGAACAACATGGGAGGAATGC
CGCCTCCTAACAACAT
Done.