Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010396.1 Kokia drynarioides strain JFW-HI SEQ_125275, 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: 2309
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31


Found at i:1650 original size:45 final size:44

Alignment explanation


    Indices: 1585--1766  Score: 211
    Period size: 45  Copynumber: 4.0  Consensus size: 44

       1575 GCATAGCTTA

                           *     * *              *    * 
       1585 TCAAGCCAAGGATATTAGCCTTAGTTTGACGAGCCACAACAATGC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCAC-GCAATAC

                                                       * 
       1630 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCATCGCAATTC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCA-CGCAATAC

                                                         
       1675 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCA-CGCAATAC

             *   **           *  * *                *    
       1720 TTAAGGAAAGGATATCAGGCTGAGTTTGACGAGCCATCGCGATAC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCA-CGCAATAC

              
       1765 TC
          1 TC

       1767 TATTCCTTCC


Statistics
Matches: 120,  Mismatches: 16, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
  45  119  0.99
  46    1  0.01

ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21


Consensus pattern (44 bp):   
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACGCAATAC

Found at i:1748 original size:90 final size:90

Alignment explanation


    Indices: 1585--1759  Score: 242
    Period size: 90  Copynumber: 1.9  Consensus size: 90

       1575 GCATAGCTTA

                           *     * *                   *       *             
       1585 TCAAGCCAAGGATATTAGCCTTAGTTTGACGAGCCACAACAATGCTCAAGCCAAGGATATCAGCC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACAACAATACTCAAGCAAAGGATATCAGCC

                                     
       1650 TCAATTTGACGAGCCATCGCAATTC
         66 TCAATTTGACGAGCCATCGCAATTC

                                                 **       *   *            * 
       1675 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACTTAAGGAAAGGATATCAGGC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACAACAATACTCAAGCAAAGGATATCAGCC

             * *                
       1740 TGAGTTTGACGAGCCATCGC
         66 TCAATTTGACGAGCCATCGC

       1760 GATACTCTAT


Statistics
Matches: 73,  Mismatches: 12, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  90   73  1.00

ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21


Consensus pattern (90 bp):   
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACAACAATACTCAAGCAAAGGATATCAGCC
TCAATTTGACGAGCCATCGCAATTC

Found at i:1803 original size:21 final size:21

Alignment explanation


    Indices: 1761--1799  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1751 AGCCATCGCG

                    *            
       1761 ATACTCTATTCCTTCCGGGCA
          1 ATACTCTACTCCTTCCGGGCA

                               
       1782 ATACTCTACTCC-TCCGGG
          1 ATACTCTACTCCTTCCGGG

       1800 GCAAATGGAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    6  0.35
  21   11  0.65

ACGTcount: A:0.18, C:0.36, G:0.15, T:0.31


Consensus pattern (21 bp):   
ATACTCTACTCCTTCCGGGCA
Done.