Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006911.1 Kokia drynarioides strain JFW-HI SEQ_121512, 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: 4499
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37


Found at i:2674 original size:13 final size:13

Alignment explanation


    Indices: 2664--2707  Score: 70
    Period size: 13  Copynumber: 3.3  Consensus size: 13

       2654 TTTCAAAAGT

                         
       2664 ACTTTTTAAAATC
          1 ACTTTTTAAAATC

                          
       2677 ACTTTTTCAAAATC
          1 ACTTTTT-AAAATC

                       * 
       2691 ACTTTTTAAAAGC
          1 ACTTTTTAAAATC

                
       2704 ACTT
          1 ACTT

       2708 CTCAAAAGCA


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  13   16  0.55
  14   13  0.45

ACGTcount: A:0.36, C:0.18, G:0.02, T:0.43


Consensus pattern (13 bp):   
ACTTTTTAAAATC

Found at i:2683 original size:14 final size:14

Alignment explanation


    Indices: 2666--2707  Score: 59
    Period size: 14  Copynumber: 3.1  Consensus size: 14

       2656 TCAAAAGTAC

                          
       2666 TTTTTAAAATCACT
          1 TTTTTAAAATCACT

                *         
       2680 TTTTCAAAATCAC-
          1 TTTTTAAAATCACT

                     *    
       2693 TTTTTAAAAGCACT
          1 TTTTTAAAATCACT

             
       2707 T
          1 T

       2708 CTCAAAAGCA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  13   11  0.46
  14   13  0.54

ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45


Consensus pattern (14 bp):   
TTTTTAAAATCACT

Found at i:2683 original size:27 final size:27

Alignment explanation


    Indices: 2652--2715  Score: 87
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       2642 TTAAACCAAG

                                    *  
       2652 CTTTTCAAAAGT-ACTTTTTAAAATCA
          1 CTTTTCAAAAGTCACTTTTTAAAAGCA

                                        
       2678 CTTTTTCAAAA-TCACTTTTTAAAAGCA
          1 C-TTTTCAAAAGTCACTTTTTAAAAGCA

               *       
       2705 CTTCTCAAAAG
          1 CTTTTCAAAAG

       2716 CAATGCTAAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 5
        0.82            0.05        0.12

Matches are distributed among these distances:
  26   10  0.30
  27   23  0.70

ACGTcount: A:0.38, C:0.19, G:0.05, T:0.39


Consensus pattern (27 bp):   
CTTTTCAAAAGTCACTTTTTAAAAGCA

Found at i:2856 original size:30 final size:30

Alignment explanation


    Indices: 2820--2879  Score: 120
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2810 ATTCTTATTT

                                          
       2820 ATATTTGCATTTACAACTGTAGACCATTAA
          1 ATATTTGCATTTACAACTGTAGACCATTAA

                                          
       2850 ATATTTGCATTTACAACTGTAGACCATTAA
          1 ATATTTGCATTTACAACTGTAGACCATTAA

       2880 TGAAGATATT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   30  1.00

ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37


Consensus pattern (30 bp):   
ATATTTGCATTTACAACTGTAGACCATTAA
Done.