Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005956.1 Kokia drynarioides strain JFW-HI SEQ_120351, 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: 30502
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:5571 original size:62 final size:61

Alignment explanation


    Indices: 5455--5575  Score: 172
    Period size: 62  Copynumber: 2.0  Consensus size: 61

       5445 ATTTTTTGGT

                               *                             *           
       5455 TCACAAATTTTAGTGACGTTAGAAATTTGGTAAAACTGTCATGAAGGCCCCTATGAGTTGC
          1 TCACAAATTTTAGTGACGTCAGAAATTTGGTAAAACTGTCATGAAGGCCACTATGAGTTGC

                 *                              *             *          
       5516 TCACACATTTTAGTGGACGTCAGAAATTTGGTAAAATTGTCATGGAA-GCTACTATGAGTT
          1 TCACAAATTTTAGT-GACGTCAGAAATTTGGTAAAACTGTCAT-GAAGGCCACTATGAGTT

       5576 AGATTGTATG


Statistics
Matches: 53,  Mismatches: 5, Indels: 3
        0.87            0.08        0.05

Matches are distributed among these distances:
  61   13  0.25
  62   37  0.70
  63    3  0.06

ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32


Consensus pattern (61 bp):   
TCACAAATTTTAGTGACGTCAGAAATTTGGTAAAACTGTCATGAAGGCCACTATGAGTTGC

Found at i:16797 original size:32 final size:32

Alignment explanation


    Indices: 16761--16824  Score: 119
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      16751 AAGTCTTTGA

                       *                    
      16761 TACTGCAACAATAAAAGGCCAACACAAATCAG
          1 TACTGCAACAAGAAAAGGCCAACACAAATCAG

                                            
      16793 TACTGCAACAAGAAAAGGCCAACACAAATCAG
          1 TACTGCAACAAGAAAAGGCCAACACAAATCAG

      16825 ACAGCAAATA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   31  1.00

ACGTcount: A:0.50, C:0.25, G:0.14, T:0.11


Consensus pattern (32 bp):   
TACTGCAACAAGAAAAGGCCAACACAAATCAG

Found at i:30346 original size:83 final size:82

Alignment explanation


    Indices: 30247--30502  Score: 316
    Period size: 92  Copynumber: 3.0  Consensus size: 82

      30237 TAAATTTAAA

                                                                             
      30247 ATATGATAAAAATTGTAATATAATAATAATTTTTATTTAAATAAATAAAATTAATAAATAATGTA
          1 ATATGATAAAAATTGTAATATAATAATAATTTTTATTTAAAT-AATAAAATTAATAAATAATGTA

                *      *      
      30312 TTGTTAAATCAGCACATT
         65 TTGTCAAATCAACACATT

              *                                                              
      30330 ATTTGATAAAAATTGTAATACAATAATAATAATAATAATTTTTATTTAAATATATAAAATTAATA
          1 ATATGATAAAAATTG--------TAAT-ATAATAATAATTTTTATTTAAATA-ATAAAATTAATA

                                   *   
      30395 AATAATGTATTGTCAAATCAACATATT
         56 AATAATGTATTGTCAAATCAACACATT

                                            *                     *          
      30422 ATATGATAAAAATTGTAATATAATAATAATTTGTACTTTAAAT-ATGAAAATTTGATAAATAATG
          1 ATATGATAAAAATTGTAATATAATAATAATTTTTA-TTTAAATAAT-AAAA-TTAATAAATAATG

                       *     
      30486 TATTGTCAAATTAACAC
         63 TATTGTCAAATCAACAC


Statistics
Matches: 151,  Mismatches: 9, Indels: 25
        0.82            0.05        0.14

Matches are distributed among these distances:
  82    2  0.01
  83   33  0.22
  84   38  0.25
  91    5  0.03
  92   73  0.48

ACGTcount: A:0.50, C:0.04, G:0.06, T:0.39


Consensus pattern (82 bp):   
ATATGATAAAAATTGTAATATAATAATAATTTTTATTTAAATAATAAAATTAATAAATAATGTAT
TGTCAAATCAACACATT

Found at i:30423 original size:92 final size:92

Alignment explanation


    Indices: 30262--30451  Score: 319
    Period size: 92  Copynumber: 2.1  Consensus size: 92

      30252 ATAAAAATTG

                                                                   *      *  
      30262 TAAT-ATAATAATAATTTTTATTTAAATAAATAAAATTAATAAATAATGTATTGTTAAATCAGCA
          1 TAATAATAATAATAATTTTTATTTAAATAAATAAAATTAATAAATAATGTATTGTCAAATCAACA

                  *                    
      30326 CATTATTTGATAAAAATTGTAATACAA
         66 CATTATATGATAAAAATTGTAATACAA

                                         *                                   
      30353 TAATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTATTGTCAAATCAACA
          1 TAATAATAATAATAATTTTTATTTAAATAAATAAAATTAATAAATAATGTATTGTCAAATCAACA

            *                       *  
      30418 TATTATATGATAAAAATTGTAATATAA
         66 CATTATATGATAAAAATTGTAATACAA

                   
      30445 TAATAAT
          1 TAATAAT

      30452 TTGTACTTTA


Statistics
Matches: 92,  Mismatches: 6, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  91    4  0.04
  92   88  0.96

ACGTcount: A:0.52, C:0.04, G:0.05, T:0.40


Consensus pattern (92 bp):   
TAATAATAATAATAATTTTTATTTAAATAAATAAAATTAATAAATAATGTATTGTCAAATCAACA
CATTATATGATAAAAATTGTAATACAA
Done.