Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga02g00844.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: 3928
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38


Found at i:3573 original size:28 final size:28

Alignment explanation


    Indices: 3540--3594  Score: 92
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       3530 GACAGTCCAC

                       *     *          
       3540 AGGGACATTCCTCCAAGTATGAGTCCGT
          1 AGGGACATTCCCCCAAGCATGAGTCCGT

                                       
       3568 AGGGACATTCCCCCAAGCATGAGTCCG
          1 AGGGACATTCCCCCAAGCATGAGTCCG

       3595 CAAGTATGTA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   25  1.00

ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20


Consensus pattern (28 bp):   
AGGGACATTCCCCCAAGCATGAGTCCGT

Found at i:3630 original size:29 final size:29

Alignment explanation


    Indices: 3552--3670  Score: 114
    Period size: 29  Copynumber: 4.1  Consensus size: 29

       3542 GGACATTCCT

                       *   *   * *      *
       3552 CCAAGTATGAGTCCGTAGGGACAT-TCCC
          1 CCAAGTATGAGCCCGCAGGTATATATCCA

                 *     *     *    *      
       3580 CCAAGCATGAGTCCGCAAGTATGTATCCA
          1 CCAAGTATGAGCCCGCAGGTATATATCCA

                    *      *             
       3609 CCAAGTATTAGCCCGTAGGTATATATCCA
          1 CCAAGTATGAGCCCGCAGGTATATATCCA

                       * *               
       3638 CCAAGTATGAGTCTGCAGGTATATATCCA
          1 CCAAGTATGAGCCCGCAGGTATATATCCA

                
       3667 CCAA
          1 CCAA

       3671 ATATAAACCT


Statistics
Matches: 73,  Mismatches: 17, Indels: 1
        0.80            0.19        0.01

Matches are distributed among these distances:
  28   18  0.25
  29   55  0.75

ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24


Consensus pattern (29 bp):   
CCAAGTATGAGCCCGCAGGTATATATCCA

Found at i:3665 original size:58 final size:57

Alignment explanation


    Indices: 3552--3670  Score: 148
    Period size: 58  Copynumber: 2.1  Consensus size: 57

       3542 GGACATTCCT

                       *               *                      *      
       3552 CCAAGTATGAGTCCGTAGGGACATTCCCCCAAGCATGAGTCCGCAAGTATGTATCCA
          1 CCAAGTATGAGCCCGTAGGGACATTCCACCAAGCATGAGTCCGCAAGTATATATCCA

                    *          * *            *       *   *           
       3609 CCAAGTATTAGCCCGTAGGTATATATCCACCAAGTATGAGTCTGCAGGTATATATCCA
          1 CCAAGTATGAGCCCGTAGGGACAT-TCCACCAAGCATGAGTCCGCAAGTATATATCCA

                
       3667 CCAA
          1 CCAA

       3671 ATATAAACCT


Statistics
Matches: 52,  Mismatches: 9, Indels: 1
        0.84            0.15        0.02

Matches are distributed among these distances:
  57   20  0.38
  58   32  0.62

ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24


Consensus pattern (57 bp):   
CCAAGTATGAGCCCGTAGGGACATTCCACCAAGCATGAGTCCGCAAGTATATATCCA

Found at i:3682 original size:29 final size:29

Alignment explanation


    Indices: 3598--3699  Score: 100
    Period size: 29  Copynumber: 3.6  Consensus size: 29

       3588 GAGTCCGCAA

                *              *    * *  
       3598 GTATGTATCCACCAAGTATTAGCCCGTAG
          1 GTATATATCCACCAAGTATAAGCCTGCAG

                               *  *      
       3627 GTATATATCCACCAAGTATGAGTCTGCAG
          1 GTATATATCCACCAAGTATAAGCCTGCAG

                           *     *       
       3656 GTATATATCCACCAAATATAAACCTGCA-
          1 GTATATATCCACCAAGTATAAGCCTGCAG

            **               
       3684 AAAT-TATCCACCAAGT
          1 GTATATATCCACCAAGT

       3700 TTTATGCTAT


Statistics
Matches: 61,  Mismatches: 12, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  27   11  0.18
  28    2  0.03
  29   48  0.79

ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26


Consensus pattern (29 bp):   
GTATATATCCACCAAGTATAAGCCTGCAG
Done.