Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006042.1 Kokia drynarioides strain JFW-HI SEQ_120505, whole genome shotgun sequence

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: 3133
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30


Found at i:1562 original size:44 final size:44

Alignment explanation


    Indices: 1437--1662  Score: 328
    Period size: 44  Copynumber: 5.2  Consensus size: 44

       1427 CTGCTAAAAA

                 *                                      
       1437 TAGCGACGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT
          1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT

                     *   **** *                         
       1481 TAGCGGCG-CTATTCCCACAAACTCCGCTATAGAACATGGTCTT
          1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT

                                     *  *               
       1524 TAGCGGCGTTTATGAGGAAAAACTCTGCAATAGAACATGGTCTT
          1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT

               *                     *             *    
       1568 TAGTGGCGTTTATGAGGAAAAACTCTGCTATAGAACATGATCTT
          1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT

               *                                        
       1612 TAGTGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT
          1 TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT

                   
       1656 TAGCGGC
          1 TAGCGGC

       1663 TTCCCTCACA


Statistics
Matches: 160,  Mismatches: 21, Indels: 2
        0.87            0.11        0.01

Matches are distributed among these distances:
  43   37  0.23
  44  123  0.77

ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28


Consensus pattern (44 bp):   
TAGCGGCGTTTATGAGGAAAAACTCCGCTATAGAACATGGTCTT

Found at i:1750 original size:43 final size:42

Alignment explanation


    Indices: 1636--1750  Score: 160
    Period size: 43  Copynumber: 2.7  Consensus size: 42

       1626 AGGAAAAACT

                  *                   *         *    *
       1636 CCGCTATAGAACATGGTCTTTAGCG-GCTTCCCTCACAAGCT
          1 CCGCTAAAGAACATGGTCTTTAGCGCACTTCCCTCAAAAGCG

                                                       
       1677 CCGCTAAAGAACATGGTCTTTAGCGACACTTCCCTCAAAAGCG
          1 CCGCTAAAGAACATGGTCTTTAGCG-CACTTCCCTCAAAAGCG

                             *             
       1720 CCGCTAAAGAACATGGTTTTTAGCAGCACTT
          1 CCGCTAAAGAACATGGTCTTTAGC-GCACTT

       1751 TTTCTACAAA


Statistics
Matches: 66,  Mismatches: 5, Indels: 4
        0.88            0.07        0.05

Matches are distributed among these distances:
  41   24  0.36
  43   41  0.62
  44    1  0.02

ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25


Consensus pattern (42 bp):   
CCGCTAAAGAACATGGTCTTTAGCGCACTTCCCTCAAAAGCG

Done.