Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g02351.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, 1000

Length: 2592
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33


Found at i:1946 original size:137 final size:137

Alignment explanation


    Indices: 1700--2122  Score: 812
    Period size: 137  Copynumber: 3.1  Consensus size: 137

       1690 GAGTAGTCTC

                                                                             
       1700 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
          1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC

                                                                             
       1765 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
         66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC

                   
       1830 ACTGTTA
        131 ACTGTTA

                                             *                               
       1837 CCCAAATGGGCTTGCATATGTTTACTGATGTTGTATGTATTTTGAAATGGGCCTATGGGCCATAC
          1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC

                                                                             
       1902 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
         66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC

                   
       1967 ACTGTTA
        131 ACTGTTA

                                                                             
       1974 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGG-CATAC
          1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC

                                                                             
       2038 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
         66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC

                   
       2103 ACTGTTA
        131 ACTGTTA

              **         
       2110 CCTGAATGGGCTT
          1 CCCAAATGGGCTT

       2123 AGGCCCAATG


Statistics
Matches: 282,  Mismatches: 4, Indels: 1
        0.98            0.01        0.00

Matches are distributed among these distances:
 136   88  0.31
 137  194  0.69

ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32


Consensus pattern (137 bp):   
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA

Found at i:1985 original size:64 final size:64

Alignment explanation


    Indices: 1780--1985  Score: 152
    Period size: 64  Copynumber: 3.1  Consensus size: 64

       1770 TCTGAATAAG

                                                                            
       1780 GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCCAAAT
          1 GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCCAAAT

                            * **             * *     *      *   *            
       1844 GGGCTTGCATATGTTTACTGATGTTGTA-TGTATTTTGAAATGGGCCTATGGGCCA-T---ACTG
          1 GGGC-T--A-A-G---GCCCA-GTT-TATTGTAATCTGAAAAGGG-CTCTGGCCCAGTACCACTG

                  **    *
       1904 TTATCTGAATAAG
         55 TTA-C-CCA-AAT

                                                                            
       1917 GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCCAAAT
          1 GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCCAAAT

                 
       1981 GGGCT
          1 GGGCT

       1986 TGCATATGTT


Statistics
Matches: 101,  Mismatches: 22, Indels: 38
        0.63            0.14        0.24

Matches are distributed among these distances:
  63   10  0.10
  64   28  0.28
  65    4  0.04
  66    1  0.01
  67    8  0.08
  68    2  0.02
  69    2  0.02
  70    8  0.08
  71    1  0.01
  72    4  0.04
  73   23  0.23
  74   10  0.10

ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30


Consensus pattern (64 bp):   
GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTGTTACCCAAAT
Done.