Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004919.1 Kokia drynarioides strain JFW-HI SEQ_118616, 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, 778

Length: 1298
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32


Found at i:413 original size:89 final size:91

Alignment explanation


    Indices: 297--464  Score: 261
    Period size: 89  Copynumber: 1.9  Consensus size: 91

        287 AAAAATGGAG

                  *  *                                          *            
        297 GAATTTTGGGGGTTTTCGAGAAAGAAAATGAGAAAGCATGAGATTATGTAAGGAAAA-AAA-TTT
          1 GAATTTAGGAGGTTTTCGAGAAAGAAAATGAGAAAGCATGAGATTATGTAAGAAAAACAAATTTT

                                      
        360 TTGGTGTTTGGTTTAGGGTTTAGGGT
         66 TTGGTGTTTGGTTTAGGGTTTAGGGT

                                                     *                       
        386 GAATTTAGGAGGTTTTC-AGGAAAGAAAATGAGAAAGCATGGGATTATGTAAGAAAAACAAATTT
          1 GAATTTAGGAGGTTTTCGA-GAAAGAAAATGAGAAAGCATGAGATTATGTAAGAAAAACAAA-TT

                           
        450 TTTTGGTGTTTGGTT
         64 TTTTGGTGTTTGGTT

        465 GTTAAGAAAA


Statistics
Matches: 71,  Mismatches: 4, Indels: 5
        0.89            0.05        0.06

Matches are distributed among these distances:
  88    1  0.01
  89   51  0.72
  90    3  0.04
  92   16  0.23

ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33


Consensus pattern (91 bp):   
GAATTTAGGAGGTTTTCGAGAAAGAAAATGAGAAAGCATGAGATTATGTAAGAAAAACAAATTTT
TTGGTGTTTGGTTTAGGGTTTAGGGT

Found at i:602 original size:29 final size:31

Alignment explanation


    Indices: 539--611  Score: 105
    Period size: 29  Copynumber: 2.4  Consensus size: 31

        529 ATTAAAATTA

                                           
        539 TTTAATAATTTTATTATTTCAAAAAAACAAT
          1 TTTAATAATTTTATTATTTCAAAAAAACAAT

                   *            *      *   
        570 TTTAATATTTTTA-TATTT-TAAAAAATAAT
          1 TTTAATAATTTTATTATTTCAAAAAAACAAT

                         
        599 TTTAATAATTTTA
          1 TTTAATAATTTTA

        612 AAATCATTTG


Statistics
Matches: 38,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  29   21  0.55
  30    5  0.13
  31   12  0.32

ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52


Consensus pattern (31 bp):   
TTTAATAATTTTATTATTTCAAAAAAACAAT
Done.