Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010022.1 Kokia drynarioides strain JFW-HI SEQ_124787, 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: 2536
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30


Found at i:571 original size:14 final size:14

Alignment explanation


    Indices: 533--573  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 14

        523 TTAACATGGA

                          
        533 GACAATGATCGTTT
          1 GACAATGATCGTTT

                   *      
        547 G---ATGCTCGTTT
          1 GACAATGATCGTTT

                          
        558 GACAATGATCGTTT
          1 GACAATGATCGTTT

              
        572 GA
          1 GA

        574 TGCTCGAGCA


Statistics
Matches: 22,  Mismatches: 2, Indels: 6
        0.73            0.07        0.20

Matches are distributed among these distances:
  11   10  0.45
  14   12  0.55

ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37


Consensus pattern (14 bp):   
GACAATGATCGTTT

Found at i:703 original size:43 final size:43

Alignment explanation


    Indices: 621--705  Score: 100
    Period size: 43  Copynumber: 2.0  Consensus size: 43

        611 ATTAACATGT

                       *          *        *  *        
        621 TAAATTATATTTCTTGACTCGTGTTAATATGGTTGCATGTTAC
          1 TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC

                           *    *                      
        664 TAAATTATATTACTTTACTCTTATTAATAT-CTTAACATGTTA
          1 TAAATTATATTACTTGACTCGTATTAATATGCTT-ACATGTTA

        706 TTAATTGTGC


Statistics
Matches: 35,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  42    2  0.06
  43   33  0.94

ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48


Consensus pattern (43 bp):   
TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC

Found at i:1405 original size:45 final size:45

Alignment explanation


    Indices: 1270--1405  Score: 173
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       1260 ACATAGCTCA

                                         *        **     
       1270 TCAAGCCAAGGATATCAGCCTCAGTTTGATGAGCCACCACAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATAC

                     *             *             *       
       1315 TCAAGCCAATGATATCAGCCTCAATTTGACGAGCCACTGTAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATAC

                 **           *  *                  *    
       1360 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCACCGTGATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATAC

             
       1405 T
          1 T

       1406 ATATTCCTCC


Statistics
Matches: 77,  Mismatches: 14, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  45   77  1.00

ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATAC

Found at i:1750 original size:28 final size:28

Alignment explanation


    Indices: 1685--1751  Score: 91
    Period size: 28  Copynumber: 2.4  Consensus size: 28

       1675 ACTTAAATTA

                 *   *             *    
       1685 TAAACCCTAAACTTAAAACCATAGACCG
          1 TAAACACTAGACTTAAAACCATAAACCG

                                         
       1713 TAAACACTAGACTTAAAACTC-TAAACCG
          1 TAAACACTAGACTTAAAAC-CATAAACCG

                       
       1741 TAAACACTAGA
          1 TAAACACTAGA

       1752 TTGATTAAGG


Statistics
Matches: 35,  Mismatches: 3, Indels: 2
        0.88            0.08        0.05

Matches are distributed among these distances:
  28   34  0.97
  29    1  0.03

ACGTcount: A:0.48, C:0.25, G:0.07, T:0.19


Consensus pattern (28 bp):   
TAAACACTAGACTTAAAACCATAAACCG
Done.