Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00281.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, 1000

Length: 2663
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29


Found at i:2035 original size:39 final size:39

Alignment explanation


    Indices: 1978--2142  Score: 215
    Period size: 39  Copynumber: 4.2  Consensus size: 39

       1968 CATGCTTCCA

                       * *          *    *         
       1978 CAGCAAATGCCTGTGGGCCAGATGAGTTCCATGTATCCT
          1 CAGCAAATGCCAGCGGGCCAGATGGGTTCAATGTATCCT

              *         *                          
       2017 CATCAAATGCCAACGGGCCAGATGGGTTCAATGTATCCT
          1 CAGCAAATGCCAGCGGGCCAGATGGGTTCAATGTATCCT

                  *    * *                          
       2056 CAGCAAGTG-CTGGGGGCCCAGATGGGTTCAATGTATCCT
          1 CAGCAAATGCCAGCGGG-CCAGATGGGTTCAATGTATCCT

                          *              *         
       2095 CAGCAAATGCCAGCTGGCCAGATGGGTTCGATGTATCCT
          1 CAGCAAATGCCAGCGGGCCAGATGGGTTCAATGTATCCT

                     
       2134 CAGCAAATG
          1 CAGCAAATG

       2143 TATGGCAACC


Statistics
Matches: 108,  Mismatches: 16, Indels: 4
        0.84            0.12        0.03

Matches are distributed among these distances:
  38    4  0.04
  39  100  0.93
  40    4  0.04

ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23


Consensus pattern (39 bp):   
CAGCAAATGCCAGCGGGCCAGATGGGTTCAATGTATCCT

Found at i:2114 original size:78 final size:78

Alignment explanation


    Indices: 1978--2142  Score: 242
    Period size: 78  Copynumber: 2.1  Consensus size: 78

       1968 CATGCTTCCA

                         *               *           *                       
       1978 CAGCAAATGCCTGTGGGCCAGATGAGTTCCATGTATCCTCATCAAATGCCAACGGGCCAGATGGG
          1 CAGCAAATGCCTGGGGGCCAGATGAGTTCAATGTATCCTCAGCAAATGCCAACGGGCCAGATGGG

                         
       2043 TTCAATGTATCCT
         66 TTCAATGTATCCT

                  *                  *                          * *          
       2056 CAGCAAGTG-CTGGGGGCCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAGCTGGCCAGATGG
          1 CAGCAAATGCCTGGGGG-CCAGATGAGTTCAATGTATCCTCAGCAAATGCCAACGGGCCAGATGG

                *         
       2120 GTTCGATGTATCCT
         65 GTTCAATGTATCCT

                     
       2134 CAGCAAATG
          1 CAGCAAATG

       2143 TATGGCAACC


Statistics
Matches: 77,  Mismatches: 9, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  77    6  0.08
  78   71  0.92

ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23


Consensus pattern (78 bp):   
CAGCAAATGCCTGGGGGCCAGATGAGTTCAATGTATCCTCAGCAAATGCCAACGGGCCAGATGGG
TTCAATGTATCCT

Done.