Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01273.M2

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: 8365
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31


Found at i:516 original size:27 final size:26

Alignment explanation


    Indices: 481--608  Score: 69
    Period size: 27  Copynumber: 4.7  Consensus size: 26

        471 GTATTGTTGC

                *                      
        481 AGTGCGTTCAACACCCAGTGGTGTTTT
          1 AGTGAGTTCAACA-CCAGTGGTGTTTT

                                 *  *   
        508 AGTGAGTTCAA-ATGCCAGTGATGCTTT
          1 AGTGAGTTCAACA--CCAGTGGTGTTTT

              **                    ** 
        535 AGCCAGTTCGAACACCAGTGGTGTCGT
          1 AGTGAGTTC-AACACCAGTGGTGTTTT

              *      *    *      **    
        562 AGCGAGTTTGAACAACAGTGGAATTTT
          1 AGTGAG-TTCAACACCAGTGGTGTTTT

              *         *       
        589 AGGGAGTTCAAAAACCAGTG
          1 AGTGAGTTC-AACACCAGTG

        609 TTATCAATGC


Statistics
Matches: 75,  Mismatches: 21, Indels: 10
        0.71            0.20        0.09

Matches are distributed among these distances:
  26    3  0.04
  27   67  0.89
  28    4  0.05
  29    1  0.01

ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27


Consensus pattern (26 bp):   
AGTGAGTTCAACACCAGTGGTGTTTT

Found at i:767 original size:81 final size:81

Alignment explanation


    Indices: 616--813  Score: 209
    Period size: 81  Copynumber: 2.4  Consensus size: 81

        606 GTGTTATCAA

                       * *                   *  **    *           *    ***   
        616 TGCTGATAGTGTTACAGCTAGTTTAAATGCTGGAAGTTTTGCTTCAAGTTCTAATGCTTTGGGTG
          1 TGCTGATAGTGCTGCAGCTAGTTTAAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG

            *               
        681 TTGCAATGAGTTCTAC
         66 CTGCAATGAGTTCTAC

                 *             *    *                                        
        697 TGCTGGTAGTGCTGCAGCTTGTTTTAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG
          1 TGCTGATAGTGCTGCAGCTAGTTTAAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG

                            
        762 CTGCAATGAGTTCTAC
         66 CTGCAATGAGTTCTAC

             *   *          * *      *           
        778 TTCTGTTAGT-CTTGCGGGTAGTTTGAATGCTGGTAG
          1 TGCTGATAGTGC-TGCAGCTAGTTTAAATGCTGGTAG

        814 TGTTGCTGAA


Statistics
Matches: 96,  Mismatches: 20, Indels: 2
        0.81            0.17        0.02

Matches are distributed among these distances:
  80    1  0.01
  81   95  0.99

ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38


Consensus pattern (81 bp):   
TGCTGATAGTGCTGCAGCTAGTTTAAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG
CTGCAATGAGTTCTAC

Found at i:2318 original size:93 final size:93

Alignment explanation


    Indices: 2159--2438  Score: 434
    Period size: 93  Copynumber: 3.0  Consensus size: 93

       2149 ATTACATGGT

                  *       *                                 *      *     *   
       2159 GGTGTTGCAACTCACGCAGAACATTTTATGCAAGCTAAAGAAACTGAGGCCAGTGTTGAGGCCCA
          1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA

                                       *
       2224 GGTTGCTTCTAAAATGATTTCTTCTGCG
         66 GGTTGCTTCTAAAATGATTTCTTCTGCA

                        *    *                                               
       2252 GGTGTTACAACTAATGCTGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA
          1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA

                      *                 
       2317 GGTTGCTTCTCAAATGATTTCTTCTGCA
         66 GGTTGCTTCTAAAATGATTTCTTCTGCA

             *               *  *                                           *
       2345 GATGTTACAACTCATGCCGAGCATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCT
          1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA

                      *                 
       2410 GGTTGCTTCTGAAATGATTTCTTCTGCA
         66 GGTTGCTTCTAAAATGATTTCTTCTGCA

             
       2438 G
          1 G

       2439 ACCATGATGT


Statistics
Matches: 172,  Mismatches: 15, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  93  172  1.00

ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29


Consensus pattern (93 bp):   
GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA
GGTTGCTTCTAAAATGATTTCTTCTGCA

Found at i:7938 original size:66 final size:66

Alignment explanation


    Indices: 7851--7980  Score: 172
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       7841 TTAACTCACC

                      *                      **                       *      
       7851 TTTTCTCTCTCTTAAGAAACTTGCAAAAAGAGATGTGATAAACA-AGAGGAGGATAGAGTGCAAA
          1 TTTTCTCTCTATTAAGAAACTTGCAAAAAGAGACATGATAAACATA-AGGAGGATAGAATGCAAA

              
       7915 CA
         65 CA

                  *                   *   *     *                           
       7917 TTTTCTTTCTATTAAGAAACTTGCAAGAAGGGACATTATAAACATAAGGAGGATAGAATGCAAA
          1 TTTTCTCTCTATTAAGAAACTTGCAAAAAGAGACATGATAAACATAAGGAGGATAGAATGCAAA

       7981 AAGAGAATTC


Statistics
Matches: 55,  Mismatches: 8, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  66   54  0.98
  67    1  0.02

ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26


Consensus pattern (66 bp):   
TTTTCTCTCTATTAAGAAACTTGCAAAAAGAGACATGATAAACATAAGGAGGATAGAATGCAAAC
A
Done.