Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga02g01328.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: 3828
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31


Found at i:3495 original size:219 final size:219

Alignment explanation


    Indices: 3116--3559  Score: 834
    Period size: 219  Copynumber: 2.0  Consensus size: 219

       3106 AGAAGCGAGG

                                                                             
       3116 TCTGTACTTTCTGATATAGCTTTGAATGATCCATCATTTGACATTCAACAACTTTGTAAAAAGTT
          1 TCTGTACTTTCTGATATAGCTTTGAATGATCCATCATTTGACATTCAACAACTTTGTAAAAAGTT

                                                         *                   
       3181 GGCAACATGCATTACTTCTACATAGCTTCTCCTTGACTAGGAAAAGCATACATCTCCATATTATA
         66 GGCAACATGCATTACTTCTACATAGCTTCTCCTTGACTAGGAAAACCATACATCTCCATATTATA

                                                                             
       3246 TTATGAACTAGAGTTATCCTTGGTTCATAGGTGTAAATTTATGAGCAGAAAAATTACATATCATT
        131 TTATGAACTAGAGTTATCCTTGGTTCATAGGTGTAAATTTATGAGCAGAAAAATTACATATCATT

                                    
       3311 CAATAACATCTGCAGCCCTAACAA
        196 CAATAACATCTGCAGCCCTAACAA

                                                                             
       3335 TCTGTACTTTCTGATATAGCTTTGAATGATCCATCATTTGACATTCAACAACTTTGTAAAAAGTT
          1 TCTGTACTTTCTGATATAGCTTTGAATGATCCATCATTTGACATTCAACAACTTTGTAAAAAGTT

                  *                                                          
       3400 GGCAACCTGCATTACTTCTACATAGCTTCTCCTTGACTAGGAAAACCATACATCTCCATATTATA
         66 GGCAACATGCATTACTTCTACATAGCTTCTCCTTGACTAGGAAAACCATACATCTCCATATTATA

                                 *             *       *                     
       3465 TTATGAACTAGAGTTATCCTTTGTTCATAGGTGTACATTTATGTGCAGAAAAATTACATATCATT
        131 TTATGAACTAGAGTTATCCTTGGTTCATAGGTGTAAATTTATGAGCAGAAAAATTACATATCATT

                                *   
       3530 CAATAACATCTGCAGCCCTAGCAA
        196 CAATAACATCTGCAGCCCTAACAA

                  
       3554 TCTGTA
          1 TCTGTA

       3560 GATGTATCGT


Statistics
Matches: 219,  Mismatches: 6, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 219  219  1.00

ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34


Consensus pattern (219 bp):   
TCTGTACTTTCTGATATAGCTTTGAATGATCCATCATTTGACATTCAACAACTTTGTAAAAAGTT
GGCAACATGCATTACTTCTACATAGCTTCTCCTTGACTAGGAAAACCATACATCTCCATATTATA
TTATGAACTAGAGTTATCCTTGGTTCATAGGTGTAAATTTATGAGCAGAAAAATTACATATCATT
CAATAACATCTGCAGCCCTAACAA

Found at i:3582 original size:6 final size:6

Alignment explanation


    Indices: 3573--3688  Score: 160
    Period size: 6  Copynumber: 19.0  Consensus size: 6

       3563 GTATCGTCTT

                                               *                     
       3573 TATATG TATATG TATATG TATATGTG TATATA TATATG TATATG TATATG
          1 TATATG TATATG TATATG TATA--TG TATATG TATATG TATATG TATATG

                               *                              *    
       3623 TATATG TATATG TATATA TATATG TATATG TATATG TATATG TGTATG
          1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG

             *      *      *    
       3671 TGTATG TGTATG TGTATG
          1 TATATG TATATG TATATG

       3689 ACCATCTAAA


Statistics
Matches: 103,  Mismatches: 5, Indels: 4
        0.92            0.04        0.04

Matches are distributed among these distances:
   6   97  0.94
   8    6  0.06

ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50


Consensus pattern (6 bp):   
TATATG

Done.