Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007234.1 Kokia drynarioides strain JFW-HI SEQ_121849, 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: 1804
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36


Found at i:608 original size:32 final size:32

Alignment explanation


    Indices: 567--746  Score: 247
    Period size: 32  Copynumber: 5.7  Consensus size: 32

        557 GTGTTGGTTG

                                            
        567 GATAGCTCTTACGAGCATACTATTTACTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                                 *    *     
        599 GATAGCTCTTACGAGCATACTGTTTATTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                              *      *      
        631 GATAGCTCTTACGAGCATGCTATTTGCTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                *       *                   
        663 GATAACTCTTACAAGCATACT-TTTACTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                               *   **       
        694 GATAGCTCTTACGAGCATATTATGCACTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                        *         
        726 GATTAGCTC-TATGAGCATACT
          1 GA-TAGCTCTTACGAGCATACT

        747 GCGAATTTAC


Statistics
Matches: 129,  Mismatches: 17, Indels: 4
        0.86            0.11        0.03

Matches are distributed among these distances:
  31   27  0.21
  32   96  0.74
  33    6  0.05

ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37


Consensus pattern (32 bp):   
GATAGCTCTTACGAGCATACTATTTACTGATT

Found at i:742 original size:95 final size:96

Alignment explanation


    Indices: 567--743  Score: 259
    Period size: 95  Copynumber: 1.9  Consensus size: 96

        557 GTGTTGGTTG

                *       *                                        * ** *      
        567 GATAGCTCTTACGAGCATACTATTTACTGATTGATAGCTCTTACGAGCATACTGTTTATTGATTG
          1 GATAACTCTTACAAGCATACTATTTACTGATTGATAGCTCTTACGAGCATACTATGCACTGATTG

                                           
        632 ATAGCTCTTACGAGCATGCTATTTGCTGATT
         66 ATAGCTCTTACGAGCATGCTATTTGCTGATT

                                                               *             
        663 GATAACTCTTACAAGCATACT-TTTACTGATTGATAGCTCTTACGAGCATATTATGCACTGATTG
          1 GATAACTCTTACAAGCATACTATTTACTGATTGATAGCTCTTACGAGCATACTATGCACTGATTG

                       *      
        727 ATTAGCTC-TATGAGCAT
         66 A-TAGCTCTTACGAGCAT

        744 ACTGCGAATT


Statistics
Matches: 72,  Mismatches: 8, Indels: 3
        0.87            0.10        0.04

Matches are distributed among these distances:
  95   47  0.65
  96   25  0.35

ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37


Consensus pattern (96 bp):   
GATAACTCTTACAAGCATACTATTTACTGATTGATAGCTCTTACGAGCATACTATGCACTGATTG
ATAGCTCTTACGAGCATGCTATTTGCTGATT

Found at i:1722 original size:21 final size:21

Alignment explanation


    Indices: 1698--1744  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       1688 CATGGTTGAG

                *             *  
       1698 CACATGGGCATGTGGAAGGGC
          1 CACACGGGCATGTGGAAGAGC

                     *     *     
       1719 CACACGGGCGTGTGGGAGAGC
          1 CACACGGGCATGTGGAAGAGC

                 
       1740 CACAC
          1 CACAC

       1745 AGCCGTGTGA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.23, C:0.26, G:0.40, T:0.11


Consensus pattern (21 bp):   
CACACGGGCATGTGGAAGAGC

Found at i:1751 original size:21 final size:21

Alignment explanation


    Indices: 1708--1753  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       1698 CACATGGGCA

                    *       * *  
       1708 TGTGGAAGGGCCACACGGGCG
          1 TGTGGAAGAGCCACACAGCCG

                 *               
       1729 TGTGGGAGAGCCACACAGCCG
          1 TGTGGAAGAGCCACACAGCCG

                
       1750 TGTG
          1 TGTG

       1754 ATCCCTGTAG


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.20, C:0.24, G:0.43, T:0.13


Consensus pattern (21 bp):   
TGTGGAAGAGCCACACAGCCG
Done.