Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00694.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: 1901
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:1872 original size:20 final size:19

Alignment explanation


    Indices: 1834--1872  Score: 51
    Period size: 20  Copynumber: 2.0  Consensus size: 19

       1824 CCAATTATTT

                          *    
       1834 ATAATTTATTTGTATTGTA
          1 ATAATTTATTTGTAATGTA

                        *       
       1853 ATAATTTGATTTTTAATGTA
          1 ATAATTT-ATTTGTAATGTA

       1873 TTTGTATCGT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19    7  0.41
  20   10  0.59

ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56


Consensus pattern (19 bp):   
ATAATTTATTTGTAATGTA

Found at i:1875 original size:31 final size:31

Alignment explanation


    Indices: 1830--1894  Score: 94
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       1820 AGTTCCAATT

                     *         *           
       1830 ATTTATAATTTATTTGTATTGTAATAATTTG
          1 ATTTATAATGTATTTGTATCGTAATAATTTG

                *                    *     
       1861 ATTTTTAATGTATTTGTATCGTAATTATTTG
          1 ATTTATAATGTATTTGTATCGTAATAATTTG

               
       1892 ATT
          1 ATT

       1895 CTACATT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58


Consensus pattern (31 bp):   
ATTTATAATGTATTTGTATCGTAATAATTTG

Found at i:1891 original size:15 final size:15

Alignment explanation


    Indices: 1839--1891  Score: 54
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       1829 TATTTATAAT

                           
       1839 TTATTTGTATTGTAA
          1 TTATTTGTATTGTAA

             *          *   
       1854 TAATTTG-ATTTTTAA
          1 TTATTTGTA-TTGTAA

                       *    
       1869 TGTATTTGTATCGTAA
          1 T-TATTTGTATTGTAA

                   
       1885 TTATTTG
          1 TTATTTG

       1892 ATTCTACATT


Statistics
Matches: 30,  Mismatches: 5, Indels: 6
        0.73            0.12        0.15

Matches are distributed among these distances:
  14    1  0.03
  15   18  0.60
  16   10  0.33
  17    1  0.03

ACGTcount: A:0.26, C:0.02, G:0.13, T:0.58


Consensus pattern (15 bp):   
TTATTTGTATTGTAA
Done.