Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002235.1 Kokia drynarioides strain JFW-HI SEQ_114236, 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: 17929
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:6692 original size:10 final size:10

Alignment explanation


    Indices: 6677--6702  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       6667 GGACAGGATA

                      
       6677 AGAGAAGAAG
          1 AGAGAAGAAG

                      
       6687 AGAGAAGAAG
          1 AGAGAAGAAG

                  
       6697 AGAGAA
          1 AGAGAA

       6703 TGAGAATGTG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (10 bp):   
AGAGAAGAAG

Found at i:15887 original size:26 final size:25

Alignment explanation


    Indices: 15858--15910  Score: 61
    Period size: 26  Copynumber: 2.1  Consensus size: 25

      15848 TTCACATAAT

                    *       *         
      15858 AGCTGATAGCAGTTCAGTCAAAGATC
          1 AGCTGATAACAGTT-AATCAAAGATC

                 *             *     
      15884 AGCTGGTAACAGTTAATCATAGATC
          1 AGCTGATAACAGTTAATCAAAGATC

              
      15909 AG
          1 AG

      15911 TTAACATAAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  25   11  0.48
  26   12  0.52

ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25


Consensus pattern (25 bp):   
AGCTGATAACAGTTAATCAAAGATC

Found at i:16699 original size:39 final size:39

Alignment explanation


    Indices: 16574--16736  Score: 177
    Period size: 39  Copynumber: 4.2  Consensus size: 39

      16564 AGTAAGACCA

                                                *  
      16574 CCAGTTCAGTATAACATTGTAGTGTTTACAGTGTCATTG
          1 CCAGTTCAGTATAACATTGTAGTGTTTACAGTGTCACTG

            *   *                                  *
      16613 TCATTTTCA-TATAACATTGTAGTGTTTACAGTGTCACTA
          1 CCA-GTTCAGTATAACATTGTAGTGTTTACAGTGTCACTG

                        * *    *           *        
      16652 CC-GATTCAGTACAGCATTTTAGTGTTTACATTGTCACTG
          1 CCAG-TTCAGTATAACATTGTAGTGTTTACAGTGTCACTG

                          **  *         *           
      16691 CCAGTTCAGTAATATTATCGTAGTGTTTGCAGTGTCACTG
          1 CCAGTTCAGT-ATAACATTGTAGTGTTTACAGTGTCACTG

                  
      16731 CCAGTT
          1 CCAGTT

      16737 ATAAACGTTC


Statistics
Matches: 101,  Mismatches: 18, Indels: 9
        0.79            0.14        0.07

Matches are distributed among these distances:
  38    4  0.04
  39   64  0.63
  40   33  0.33

ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39


Consensus pattern (39 bp):   
CCAGTTCAGTATAACATTGTAGTGTTTACAGTGTCACTG
Done.