Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002207.1 Kokia drynarioides strain JFW-HI SEQ_114195, 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, 734

Length: 1224
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27


Found at i:418 original size:29 final size:29

Alignment explanation


    Indices: 386--442  Score: 69
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        376 GGGAAAATTT

                *                        
        386 AGGGTTAAAAAAAGAATTTTTAGAAGTTC
          1 AGGGATAAAAAAAGAATTTTTAGAAGTTC

                      ** *       *      
        415 AGGGATAAAAGTATAATTTTTGGAAGTT
          1 AGGGATAAAAAAAGAATTTTTAGAAGTT

        443 TCGAGGCCAA


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  29   23  1.00

ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33


Consensus pattern (29 bp):   
AGGGATAAAAAAAGAATTTTTAGAAGTTC

Found at i:466 original size:30 final size:28

Alignment explanation


    Indices: 430--590  Score: 119
    Period size: 29  Copynumber: 5.5  Consensus size: 28

        420 TAAAAGTATA

                                          
        430 ATTTTTGGAAGTTTCGAGGCCAAAAATGAG
          1 ATTTTTGGAAGTTTCG-GGCCAAAAATG-G

                   *       *   *          
        460 ATTTTTGAAAGTTTTGGGGTC-AAAATGGG
          1 ATTTTTGGAAG-TTTCGGGCCAAAAAT-GG

             *            *   **     *  
        489 AGTTTTGGAAGTTTTGGGGTAAAAACGG
          1 ATTTTTGGAAGTTTCGGGCCAAAAATGG

                               *          
        517 AATTTTTGGAAGTTTCGGGTCAAAAATGGG
          1 -ATTTTTGGAAGTTTCGGGCCAAAAAT-GG

                       *  *     *        
        547 ATTTTTGGAA-ATTGGAGGCTAAAAATGG
          1 ATTTTTGGAAGTTTCG-GGCCAAAAATGG

                            
        575 AATTTTTGGATAGTTT
          1 -ATTTTTGGA-AGTTT

        591 AGGGACCTCC


Statistics
Matches: 103,  Mismatches: 19, Indels: 17
        0.74            0.14        0.12

Matches are distributed among these distances:
  28   13  0.13
  29   67  0.65
  30   17  0.17
  31    6  0.06

ACGTcount: A:0.30, C:0.05, G:0.29, T:0.35


Consensus pattern (28 bp):   
ATTTTTGGAAGTTTCGGGCCAAAAATGG

Found at i:530 original size:58 final size:59

Alignment explanation


    Indices: 460--590  Score: 162
    Period size: 58  Copynumber: 2.2  Consensus size: 59

        450 CAAAAATGAG

                   *       *                          *                  
        460 ATTTTTGAAAGTTTTGGGGTC-AAAATGGGAGTTTTGGAAGTTTTGG-GG-TAAAAACGGA
          1 ATTTTTGGAAGTTTTCGGGTCAAAAATGGGAGTTTTGGAA--ATTGGAGGCTAAAAACGGA

                                           *                       *   
        518 ATTTTTGGAAG-TTTCGGGTCAAAAATGGGATTTTTGGAAATTGGAGGCTAAAAATGGA
          1 ATTTTTGGAAGTTTTCGGGTCAAAAATGGGAGTTTTGGAAATTGGAGGCTAAAAACGGA

                           
        576 ATTTTTGGATAGTTT
          1 ATTTTTGGA-AGTTT

        591 AGGGACCTCC


Statistics
Matches: 63,  Mismatches: 5, Indels: 8
        0.83            0.07        0.11

Matches are distributed among these distances:
  56    4  0.06
  57   10  0.16
  58   45  0.71
  59    2  0.03
  60    2  0.03

ACGTcount: A:0.30, C:0.04, G:0.30, T:0.37


Consensus pattern (59 bp):   
ATTTTTGGAAGTTTTCGGGTCAAAAATGGGAGTTTTGGAAATTGGAGGCTAAAAACGGA
Done.