Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01065.N2

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, 612

Length: 1021
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27


Found at i:800 original size:39 final size:39

Alignment explanation


    Indices: 725--880  Score: 208
    Period size: 39  Copynumber: 4.0  Consensus size: 39

        715 GATGTGTATG

                                           *       
        725 AATGTGCGAATTGTGATATCC-GGCTAAGCCTGAAGGCA
          1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA

                                                   
        763 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
          1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA

             *           *                         *
        802 ATTGTGCGAGA-TATGATATCCGGGCTAAGCCCGAAGGCG
          1 AATGTGCGA-ATTGTGATATCCGGGCTAAGCCCGAAGGCA

             *       *              *        *      
        841 ATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCAAAGGCA
          1 AATGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCA

        881 TTTGTGCGGG


Statistics
Matches: 105,  Mismatches: 9, Indels: 6
        0.88            0.08        0.05

Matches are distributed among these distances:
  38   21  0.20
  39   75  0.71
  40    9  0.09

ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23


Consensus pattern (39 bp):   
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA

Found at i:855 original size:78 final size:79

Alignment explanation


    Indices: 738--920  Score: 235
    Period size: 78  Copynumber: 2.3  Consensus size: 79

        728 GTGCGAATTG

                              *      *                                 *     
        738 TGATATCC-GGCTAAGCCTGAAGGCAAATGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGC
          1 TGATATCCGGGCTAAGCCCGAAGGCGAATGTGCGAATTGTGATATCCGGGCTAAGTCCCAAAGGC

                          
        801 AATTGTGCGAGATA
         66 AATTGTGCGAGATA

                                       *       *              *              
        815 TGATATCCGGGCTAAGCCCGAAGGCGATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCAAAGGC
          1 TGATATCCGGGCTAAGCCCGAAGGCGAATGTGCGAATTGTGATATCCGGGCTAAGTCCCAAAGGC

             *       * *  
        880 ATTTGTGCGGGTTA
         66 AATTGTGCGAGATA

             *   *        *            
        894 TCATAACCGGGCTATGTCCCGAAGGCG
          1 TGATATCCGGGCTAAG-CCCGAAGGCG

        921 TTTGAACGAG


Statistics
Matches: 91,  Mismatches: 12, Indels: 3
        0.86            0.11        0.03

Matches are distributed among these distances:
  77    8  0.09
  78   41  0.45
  79   32  0.35
  80   10  0.11

ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23


Consensus pattern (79 bp):   
TGATATCCGGGCTAAGCCCGAAGGCGAATGTGCGAATTGTGATATCCGGGCTAAGTCCCAAAGGC
AATTGTGCGAGATA

Found at i:904 original size:40 final size:39

Alignment explanation


    Indices: 727--924  Score: 202
    Period size: 39  Copynumber: 5.1  Consensus size: 39

        717 TGTGTATGAA

                   *  *                  *       **
        727 TGTGCGAATTGTGATATCC-GGCTAAGCCTGAAGGCAAA
          1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCATT

                   *  *                          * 
        765 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
          1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCATT

                    *                               
        804 TGTGCGAGATATGATATCCGGGCTAAGCCCGAAGGCGA-T
          1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGC-ATT

                      *           *        *        
        843 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCAAAGGCATT
          1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCATT

                  *     *   *        *           *  
        883 TGTGCGGGTTATCATAACCGGGCTATGTCCCGAAGGCGTT
          1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCATT

              
        923 TG
          1 TG

        925 AACGAGTAGC


Statistics
Matches: 139,  Mismatches: 17, Indels: 6
        0.86            0.10        0.04

Matches are distributed among these distances:
  38   19  0.14
  39   76  0.55
  40   44  0.32

ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25


Consensus pattern (39 bp):   
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCATT

Found at i:946 original size:79 final size:78

Alignment explanation


    Indices: 775--947  Score: 197
    Period size: 79  Copynumber: 2.2  Consensus size: 78

        765 TGTGCGAATT

                        *       *                    *   *                   
        775 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGATATGATATCCGGGCTAAGCCCGAAGGC
          1 GTGATATCCGGGTTAAGCCCAAAGGCAATTGTGCGAGATATCATAACCGGGCTAAGCCCGAAGGC

                 **     *
        840 GATTGTGCGAGTT
         66 GATTGAACGAGTA

                                        *       * *                *         
        853 GTGATATCCGGGTTAAGTCCCAAAGGCATTTGTGCGGGTTATCATAACCGGGCTATGTCCCGAAG
          1 GTGATATCCGGGTTAAG-CCCAAAGGCAATTGTGCGAGATATCATAACCGGGCTAAG-CCCGAAG

               *           
        918 GCGTTTGAACGAGTA
         64 GCGATTGAACGAGTA

                             
        933 GCT-ATATCC-GGTTAA
          1 G-TGATATCCGGGTTAA

        948 ACTCCGAAGG


Statistics
Matches: 80,  Mismatches: 12, Indels: 5
        0.82            0.12        0.05

Matches are distributed among these distances:
  78   16  0.20
  79   38  0.47
  80   25  0.31
  81    1  0.01

ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25


Consensus pattern (78 bp):   
GTGATATCCGGGTTAAGCCCAAAGGCAATTGTGCGAGATATCATAACCGGGCTAAGCCCGAAGGC
GATTGAACGAGTA
Done.