Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01206.P1

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: 3163
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33


Found at i:454 original size:21 final size:21

Alignment explanation


    Indices: 430--531  Score: 114
    Period size: 21  Copynumber: 4.9  Consensus size: 21

        420 AAAAACCCTA

                  *              
        430 TTATACCATATGCGAACCATG
          1 TTATACTATATGCGAACCATG

                 *          * *  
        451 TTATATTATATGCGAAACTTG
          1 TTATACTATATGCGAACCATG

                        *  *  * *
        472 TTATACTATATGAGATCCTTA
          1 TTATACTATATGCGAACCATG

                                 
        493 TTATACTATATGCGAACCATG
          1 TTATACTATATGCGAACCATG

                     *   *    
        514 TTATACTATGTGCAAACC
          1 TTATACTATATGCGAACC

        532 CATGCTATTA


Statistics
Matches: 66,  Mismatches: 15, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  21   66  1.00

ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36


Consensus pattern (21 bp):   
TTATACTATATGCGAACCATG

Found at i:705 original size:17 final size:17

Alignment explanation


    Indices: 685--722  Score: 67
    Period size: 17  Copynumber: 2.2  Consensus size: 17

        675 CGAGCTCTGC

                             
        685 TATATTGCGAGCCCTAT
          1 TATATTGCGAGCCCTAT

                   *         
        702 TATATTGTGAGCCCTAT
          1 TATATTGCGAGCCCTAT

                
        719 TATA
          1 TATA

        723 CTATGAATGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39


Consensus pattern (17 bp):   
TATATTGCGAGCCCTAT

Found at i:1563 original size:22 final size:22

Alignment explanation


    Indices: 1537--1581  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1527 ATGAGAAATG

                 *                 
       1537 GGTTGTGATATGT-TACATTGAT
          1 GGTTGCGATATGTCTA-ATTGAT

                     *            
       1559 GGTTGCGATCTGTCTAATTGAT
          1 GGTTGCGATATGTCTAATTGAT

             
       1581 G
          1 G

       1582 TATGAATGGG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  22   18  0.90
  23    2  0.10

ACGTcount: A:0.20, C:0.09, G:0.29, T:0.42


Consensus pattern (22 bp):   
GGTTGCGATATGTCTAATTGAT

Found at i:1945 original size:27 final size:27

Alignment explanation


    Indices: 1887--1952  Score: 71
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       1877 AATAAGAGAT

                     **               *
       1887 CGTAGGGTAAATTGTGAACTAGCGATT
          1 CGTAGGGTAGGTTGTGAACTAGCGATC

            *                           
       1914 TGTAGGGTAGGTTGTGAACTAG-GTATC
          1 CGTAGGGTAGGTTGTGAACTAGCG-ATC

                   *    
       1941 CGTAGGGCAGGT
          1 CGTAGGGTAGGT

       1953 CGCGAGCTAG


Statistics
Matches: 32,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  26    1  0.03
  27   31  0.97

ACGTcount: A:0.24, C:0.11, G:0.36, T:0.29


Consensus pattern (27 bp):   
CGTAGGGTAGGTTGTGAACTAGCGATC

Found at i:2683 original size:12 final size:12

Alignment explanation


    Indices: 2651--2684  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       2641 GTGGTAGTGG

                    **  
       2651 TGATGATGACGA
          1 TGATGATGGTGA

                        
       2663 TGATGATGGTGA
          1 TGATGATGGTGA

                      
       2675 TGATGATGGT
          1 TGATGATGGT

       2685 TCTAAAATGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.26, C:0.03, G:0.38, T:0.32


Consensus pattern (12 bp):   
TGATGATGGTGA
Done.