Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002754.1 Kokia drynarioides strain JFW-HI SEQ_115070, 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: 5973
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37


Found at i:1371 original size:18 final size:18

Alignment explanation


    Indices: 1314--1371  Score: 57
    Period size: 17  Copynumber: 3.2  Consensus size: 18

       1304 TACTGATTTT

                      *     *  
       1314 TTTTTATAAAATTAGTGAA
          1 TTTTTATAAATTTA-TTAA

                              *
       1333 TTTCTTA-AAATTTATT-T
          1 TTT-TTATAAATTTATTAA

                              
       1350 TTTTTATAAATTTATTAA
          1 TTTTTATAAATTTATTAA

                
       1368 TTTT
          1 TTTT

       1372 CATATAACTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 7
        0.74            0.09        0.16

Matches are distributed among these distances:
  16    3  0.09
  17   12  0.38
  18    5  0.16
  19    9  0.28
  20    3  0.09

ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60


Consensus pattern (18 bp):   
TTTTTATAAATTTATTAA

Found at i:2658 original size:31 final size:31

Alignment explanation


    Indices: 2623--2692  Score: 131
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2613 TTCAAACATG

                                           
       2623 AGTGACTAAAATGTAACCTGAAGCAAACAAA
          1 AGTGACTAAAATGTAACCTGAAGCAAACAAA

                                *          
       2654 AGTGACTAAAATGTAACCTGGAGCAAACAAA
          1 AGTGACTAAAATGTAACCTGAAGCAAACAAA

                    
       2685 AGTGACTA
          1 AGTGACTA

       2693 TTTTTATAAT


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   38  1.00

ACGTcount: A:0.49, C:0.16, G:0.19, T:0.17


Consensus pattern (31 bp):   
AGTGACTAAAATGTAACCTGAAGCAAACAAA

Found at i:2785 original size:14 final size:14

Alignment explanation


    Indices: 2766--2805  Score: 57
    Period size: 13  Copynumber: 3.0  Consensus size: 14

       2756 TTTGGACTTC

                          
       2766 AAAGGAAAAAAAAA
          1 AAAGGAAAAAAAAA

                        * 
       2780 AAAGG-AAAAAAGA
          1 AAAGGAAAAAAAAA

                          
       2793 AAA-GAAAAAAAAA
          1 AAAGGAAAAAAAAA

       2806 CGAAGGCAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  12    1  0.04
  13   17  0.74
  14    5  0.22

ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00


Consensus pattern (14 bp):   
AAAGGAAAAAAAAA
Done.