Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006245.1 Kokia drynarioides strain JFW-HI SEQ_120816, 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: 14634
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36


Found at i:1625 original size:15 final size:16

Alignment explanation


    Indices: 1600--1630  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

       1590 TACCCATAGA

                            
       1600 AAAGAGAAGAGAAGAG
          1 AAAGAGAAGAGAAGAG

                            
       1616 AAAG-GAAGAGAAGAG
          1 AAAGAGAAGAGAAGAG

       1631 GAATGGGGAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15   11  0.73
  16    4  0.27

ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00


Consensus pattern (16 bp):   
AAAGAGAAGAGAAGAG

Found at i:8345 original size:23 final size:23

Alignment explanation


    Indices: 8315--8358  Score: 72
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       8305 TATTACATAT

                                    
       8315 ATTATATACATA-AATATATTTCA
          1 ATTATATACATACAA-ATATTTCA

                                 
       8338 ATTATATACATACAAATATTT
          1 ATTATATACATACAAATATTT

       8359 TATGTGAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  23   18  0.90
  24    2  0.10

ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43


Consensus pattern (23 bp):   
ATTATATACATACAAATATTTCA

Found at i:11572 original size:71 final size:71

Alignment explanation


    Indices: 11456--11668  Score: 408
    Period size: 71  Copynumber: 3.0  Consensus size: 71

      11446 ACAAACAATC

                                                                             
      11456 CAAATATTTAAAGGTATAAAGCCAGTGAAGATACAAATGAAGTATTTTTTGGACTTGCAGTCCTG
          1 CAAATATTTAAAGGTATAAAGCCAGTGAAGATACAAATGAAGTATTTTTTGGACTTGCAGTCCTG

                  
      11521 ACATTG
         66 ACATTG

                                                                  *          
      11527 CAAATATTTAAAGGTATAAAGCCAGTGAAGATACAAATGAAGTATTTTTTGGACCTGCAGTCCTG
          1 CAAATATTTAAAGGTATAAAGCCAGTGAAGATACAAATGAAGTATTTTTTGGACTTGCAGTCCTG

                  
      11592 ACATTG
         66 ACATTG

                                                                   *         
      11598 CAAATATTTAAAGGTATAAAGCCAGTGAAGATACAAATGAAGTATTTTTTGGACTAGCAGTCCTG
          1 CAAATATTTAAAGGTATAAAGCCAGTGAAGATACAAATGAAGTATTTTTTGGACTTGCAGTCCTG

                  
      11663 ACATTG
         66 ACATTG

      11669 ATTATAAAAA


Statistics
Matches: 139,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  71  139  1.00

ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30


Consensus pattern (71 bp):   
CAAATATTTAAAGGTATAAAGCCAGTGAAGATACAAATGAAGTATTTTTTGGACTTGCAGTCCTG
ACATTG

Found at i:11770 original size:61 final size:61

Alignment explanation


    Indices: 11669--11791  Score: 228
    Period size: 61  Copynumber: 2.0  Consensus size: 61

      11659 CCTGACATTG

                                                                         
      11669 ATTATAAAAAAATATAATATTCTTTTGTGATGGATACAATAACCTTTAGATATATTATTAA
          1 ATTATAAAAAAATATAATATTCTTTTGTGATGGATACAATAACCTTTAGATATATTATTAA

                                             * *                         
      11730 ATTATAAAAAAATATAATATTCTTTTGTGATGGGTGCAATAACCTTTAGATATATTATTAA
          1 ATTATAAAAAAATATAATATTCTTTTGTGATGGATACAATAACCTTTAGATATATTATTAA

             
      11791 A
          1 A

      11792 CTGACAGTTC


Statistics
Matches: 60,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  61   60  1.00

ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41


Consensus pattern (61 bp):   
ATTATAAAAAAATATAATATTCTTTTGTGATGGATACAATAACCTTTAGATATATTATTAA
Done.