Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00169.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: 2726
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.24


Found at i:620 original size:48 final size:49

Alignment explanation


    Indices: 547--817  Score: 268
    Period size: 48  Copynumber: 5.5  Consensus size: 49

        537 GCAACCGCCG

                          *     *                     *      
        547 CCGCCTCCGAAAGAGACGCAGACGCTGTTTATGCAACAGCCACCGT-CT
          1 CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACAGCCAGCGTCCT

            *             *                      *   *       
        595 GCGCCTCCGAAAGAGACGCAAACGCTGTTTATGCAACCGCCTGC-TCCT
          1 CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACAGCCAGCGTCCT

                    *  *        *   *          * *   *       
        643 CCGCCTCCTAAGGAAACGCAGACGTTGTTTATGCAGCCGCCGGC-TCCT
          1 CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACAGCCAGCGTCCT

                       *                              *       
        691 CCGCCTCCGAAGGAAACGCAAACGCTGTTTATGCAACCA-CCGGC-TCCT
          1 CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAA-CAGCCAGCGTCCT

                                                            *       
        739 CCGCCTCCGAAAGAAACGCAAACGCAAACGCTGTTTATGCAACCA-CCGGCG-CCT
          1 CCGCCTCC----GAAA-G-AAACGCAAACGCTGTTTATGCAA-CAGCCAGCGTCCT

                                     
        793 CCGCCTCCGAAAGAAACGCAAACGC
          1 CCGCCTCCGAAAGAAACGCAAACGC

        818 AAACGCTGTT


Statistics
Matches: 195,  Mismatches: 19, Indels: 18
        0.84            0.08        0.08

Matches are distributed among these distances:
  47    1  0.01
  48  142  0.73
  49    2  0.01
  50    4  0.02
  52    3  0.02
  53    1  0.01
  54   42  0.22

ACGTcount: A:0.25, C:0.37, G:0.22, T:0.16


Consensus pattern (49 bp):   
CCGCCTCCGAAAGAAACGCAAACGCTGTTTATGCAACAGCCAGCGTCCT

Found at i:696 original size:96 final size:96

Alignment explanation


    Indices: 547--817  Score: 321
    Period size: 96  Copynumber: 2.8  Consensus size: 96

        537 GCAACCGCCG

                           *                      *   **      *             *
        547 CCGCCTCCGAAA-GAGACGCAGACGCTGTTTATGCAACAGCCACCGT-CTGCGCCTCCGAAAGAG
          1 CCGCCTCC-AAAGGAAACGCAGACGCTGTTTATGCAACCGCCGGC-TCCTCCGCCTCCGAAAGAA

                                   *  *      
        610 ACGCAAACGCTGTTTATGCAACCGCCTGCTCCT
         64 ACGCAAACGCTGTTTATGCAACCACCGGCTCCT

                    *               *          *                       *     
        643 CCGCCTCCTAAGGAAACGCAGACGTTGTTTATGCAGCCGCCGGCTCCTCCGCCTCCGAAGGAAAC
          1 CCGCCTCCAAAGGAAACGCAGACGCTGTTTATGCAACCGCCGGCTCCTCCGCCTCCGAAAGAAAC

                                           
        708 GCAAACGCTGTTTATGCAACCACCGGCTCCT
         66 GCAAACGCTGTTTATGCAACCACCGGCTCCT

                                      *                 *     *              
        739 CCGCCTCCGAAAGAAACGCAAACGCAAACGCTGTTTATGCAACCACCGGCGCCTCCGCCTCCGAA
          1 CCGCCTCC-AAAG----G-AAACGCAGACGCTGTTTATGCAACCGCCGGCTCCTCCGCCTCCGAA

                          
        804 AGAAACGCAAACGC
         60 AGAAACGCAAACGC

        818 AAACGCTGTT


Statistics
Matches: 148,  Mismatches: 19, Indels: 10
        0.84            0.11        0.06

Matches are distributed among these distances:
  95    3  0.02
  96   87  0.59
  97    3  0.02
 101    1  0.01
 102   54  0.36

ACGTcount: A:0.25, C:0.37, G:0.22, T:0.16


Consensus pattern (96 bp):   
CCGCCTCCAAAGGAAACGCAGACGCTGTTTATGCAACCGCCGGCTCCTCCGCCTCCGAAAGAAAC
GCAAACGCTGTTTATGCAACCACCGGCTCCT

Found at i:714 original size:54 final size:54

Alignment explanation


    Indices: 610--834  Score: 294
    Period size: 48  Copynumber: 4.4  Consensus size: 54

        600 TCCGAAAGAG

                                   *  *               *           
        610 ACGCAAACGCTGTTTATGCAACCGCCTGCTCCTCCGCCTCC-TAAG----G-AA
          1 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA

                 *   *          *  *                              
        658 ACGCAGACGTTGTTTATGCAGCCGCCGGCTCCTCCGCCTCCG-AAG----G-AA
          1 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA

                                                                  
        706 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA
          1 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA

                                         *                        
        760 ACGCAAACGCTGTTTATGCAACCACCGGCGCCTCCGCCTCCGAAAGAAACGCAA
          1 ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA

                                 
        814 ACGCAAACGCTGTTTATGCAA
          1 ACGCAAACGCTGTTTATGCAA

        835 TCGCCGCCAA


Statistics
Matches: 161,  Mismatches: 9, Indels: 8
        0.90            0.05        0.04

Matches are distributed among these distances:
  48   81  0.50
  49    3  0.02
  53    1  0.01
  54   76  0.47

ACGTcount: A:0.26, C:0.36, G:0.21, T:0.17


Consensus pattern (54 bp):   
ACGCAAACGCTGTTTATGCAACCACCGGCTCCTCCGCCTCCGAAAGAAACGCAA
Done.