Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00809.N1

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: 6445
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Found at i:3323 original size:20 final size:20

Alignment explanation


    Indices: 3300--3337  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3290 CACTTCCAAA

                    *           
       3300 TACAAAATTTTAAAAATCAT
          1 TACAAAATATTAAAAATCAT

                              
       3320 TACAAAATATTAAAAATC
          1 TACAAAATATTAAAAATC

       3338 GCGAATAAAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32


Consensus pattern (20 bp):   
TACAAAATATTAAAAATCAT

Found at i:3740 original size:27 final size:27

Alignment explanation


    Indices: 3698--3837  Score: 147
    Period size: 27  Copynumber: 5.2  Consensus size: 27

       3688 GAGGAAGCGT

                      *                
       3698 TCTGGTGGCTATGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

               *            *          
       3725 TCTAGTGGCTCTGCCATAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                              *       *
       3752 TCTGGTGGCTCTGCCACATATATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

             *              ** *        
       3779 TTTGGTGGCTCTGCCAGGATTATCTGTA
          1 TCTGGTGGCTCTGCCACAAATATCTG-A

                   *     *     *      *
       3807 TCTGGTGACTCTGTCAC-ATTATCTGC
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                 
       3833 TCTGG
          1 TCTGG

       3838 CAGCCATGCT


Statistics
Matches: 94,  Mismatches: 18, Indels: 3
        0.82            0.16        0.03

Matches are distributed among these distances:
  26    5  0.05
  27   76  0.81
  28   13  0.14

ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36


Consensus pattern (27 bp):   
TCTGGTGGCTCTGCCACAAATATCTGA

Found at i:3787 original size:54 final size:55

Alignment explanation


    Indices: 3698--3831  Score: 164
    Period size: 54  Copynumber: 2.5  Consensus size: 55

       3688 GAGGAAGCGT

                      *       *                        *           
       3698 TCTGGTGGCTATGCCACAAATATCTGATCTAGTGGCTCTGCCATAAATATCTG-A
          1 TCTGGTGGCTCTGCCACATATATCTGATCTAGTGGCTCTGCCAGAAATATCTGTA

                                      * * *             * *        
       3752 TCTGGTGGCTCTGCCACATATATCTGTTTTGGTGGCTCTGCCAGGATTATCTGTA
          1 TCTGGTGGCTCTGCCACATATATCTGATCTAGTGGCTCTGCCAGAAATATCTGTA

                   *     *            
       3807 TCTGGTGACTCTGTCACAT-TATCTG
          1 TCTGGTGGCTCTGCCACATATATCTG

       3832 CTCTGGCAGC


Statistics
Matches: 69,  Mismatches: 10, Indels: 2
        0.85            0.12        0.02

Matches are distributed among these distances:
  54   51  0.74
  55   18  0.26

ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36


Consensus pattern (55 bp):   
TCTGGTGGCTCTGCCACATATATCTGATCTAGTGGCTCTGCCAGAAATATCTGTA

Found at i:4586 original size:27 final size:27

Alignment explanation


    Indices: 4548--4670  Score: 147
    Period size: 27  Copynumber: 4.5  Consensus size: 27

       4538 AAGCGTTCTG

                  *            *       
       4548 GTGGCTATGCCACAAATATATGATCTA
          1 GTGGCTCTGCCACAAATATCTGATCTA

                                      *
       4575 GTGGCTCTGCCACAAATATCTGATCTG
          1 GTGGCTCTGCCACAAATATCTGATCTA

                          *       *   *
       4602 GTGGCTCTGCCACATATATCTGTTCTG
          1 GTGGCTCTGCCACAAATATCTGATCTA

                         * *            
       4629 GTGGCTCTGCCACGATTATCTGTATCTA
          1 GTGGCTCTGCCACAAATATCTG-ATCTA

               *     *    
       4657 GTGACTCTGTCACA
          1 GTGGCTCTGCCACA

       4671 TTATCTGTTC


Statistics
Matches: 82,  Mismatches: 13, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
  27   68  0.83
  28   14  0.17

ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33


Consensus pattern (27 bp):   
GTGGCTCTGCCACAAATATCTGATCTA

Found at i:4633 original size:54 final size:55

Alignment explanation


    Indices: 4544--4683  Score: 176
    Period size: 54  Copynumber: 2.6  Consensus size: 55

       4534 GAGGAAGCGT

                      *       *    *  *   *                        
       4544 TCTGGTGGCTATGCCACAAATATATGATCTAGTGGCTCTGCCACAAATATCTG-A
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

                                                        * *        
       4598 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

               *   *     *                  
       4653 TCTAGTGACTCTGTCACAT-TATCTGTTCTGG
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG

       4684 CAGCCATGCT


Statistics
Matches: 75,  Mismatches: 10, Indels: 2
        0.86            0.11        0.02

Matches are distributed among these distances:
  54   58  0.77
  55   17  0.23

ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35


Consensus pattern (55 bp):   
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA

Done.