Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014870.1 Kokia drynarioides strain JFW-HI SEQ_129913, 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: 345502
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32

Warning! 6 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:342557 original size:36 final size:36

Alignment explanation


    Indices: 342487--342558  Score: 92
    Period size: 36  Copynumber: 2.0  Consensus size: 36

     342477 TATTGTACTA

                           *         *   *      
     342487 GCTCGTTAGAGCATATTGGCTCATTTGAGTATATTG
          1 GCTCGTTAGAGCATACTGGCTCATTAGAGCATATTG

                   *                             
     342523 GCTCGTTTGAGCATACTGGCTCGA-TAGAGCATATTG
          1 GCTCGTTAGAGCATACTGGCTC-ATTAGAGCATATTG

     342559 ACTTATTAGA


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  36   30  0.97
  37    1  0.03

ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35


Consensus pattern (36 bp):   
GCTCGTTAGAGCATACTGGCTCATTAGAGCATATTG

Found at i:342622 original size:19 final size:19

Alignment explanation


    Indices: 342589--342662  Score: 96
    Period size: 19  Copynumber: 3.9  Consensus size: 19

     342579 TCGTTTTAGC

                      *        
     342589 ATACTGGCTCTTAAGAGCG
          1 ATACTGGCTCGTAAGAGCG

              *    *           
     342608 ATGCTGGATCGTAAGAGC-
          1 ATACTGGCTCGTAAGAGCG

                              * 
     342626 ATTACTGGCTCGTAAGAGTG
          1 A-TACTGGCTCGTAAGAGCG

                             
     342646 ATACTGGCTCGTAAGAG
          1 ATACTGGCTCGTAAGAG

     342663 AAAATTACTA


Statistics
Matches: 47,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  18    1  0.02
  19   45  0.96
  20    1  0.02

ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26


Consensus pattern (19 bp):   
ATACTGGCTCGTAAGAGCG

Found at i:342633 original size:38 final size:37

Alignment explanation


    Indices: 342586--342662  Score: 109
    Period size: 38  Copynumber: 2.1  Consensus size: 37

     342576 AACTCGTTTT

                         *          *            
     342586 AGCATACTGGCTCTTAAGAGCGATGCTGGATCGTAAG
          1 AGCATACTGGCTCGTAAGAGCGATACTGGATCGTAAG

                                 *        *       
     342623 AGCATTACTGGCTCGTAAGAGTGATACTGGCTCGTAAG
          1 AGCA-TACTGGCTCGTAAGAGCGATACTGGATCGTAAG

              
     342661 AG
          1 AG

     342663 AAAATTACTA


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  37    4  0.11
  38   31  0.89

ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25


Consensus pattern (37 bp):   
AGCATACTGGCTCGTAAGAGCGATACTGGATCGTAAG

Done.