Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008688.1 Kokia drynarioides strain JFW-HI SEQ_123370, 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: 3917
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34


Found at i:1910 original size:36 final size:36

Alignment explanation


    Indices: 1798--1893  Score: 183
    Period size: 36  Copynumber: 2.7  Consensus size: 36

       1788 ATATAATCAG

                                                
       1798 TCACATGGCATGAAAAACATACCCACATATTTACTA
          1 TCACATGGCATGAAAAACATACCCACATATTTACTA

                                                
       1834 TCACATGGCATGAAAAACATACCCACATATTTACTA
          1 TCACATGGCATGAAAAACATACCCACATATTTACTA

                          *         
       1870 TCACATGGCATGAATAACATACCC
          1 TCACATGGCATGAAAAACATACCC

       1894 TCACATTCAC


Statistics
Matches: 59,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  36   59  1.00

ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24


Consensus pattern (36 bp):   
TCACATGGCATGAAAAACATACCCACATATTTACTA

Found at i:3795 original size:29 final size:29

Alignment explanation


    Indices: 3752--3857  Score: 108
    Period size: 30  Copynumber: 3.6  Consensus size: 29

       3742 GATCAGGGGT

                                     *     
       3752 AAAATGGTAATTTTTGGAAAATTTGCGGTTA
          1 AAAATGG-AA-TTTTGGAAAATTTGAGGTTA

                                      *  
       3783 AAAATGGAATTTTGG-AAATTTGAGGGT-
          1 AAAATGGAATTTTGGAAAATTTGAGGTTA

                   * *           * *       
       3810 AAAATAGTATTTTTAGGAAAAATCGAGGTTA
          1 AAAAT-GGAATTTT-GGAAAATTTGAGGTTA

                             
       3841 AAAATGGAATTTTGGAA
          1 AAAATGGAATTTTGGAA

       3858 GTTCGGGGTA


Statistics
Matches: 62,  Mismatches: 9, Indels: 10
        0.77            0.11        0.12

Matches are distributed among these distances:
  27    5  0.08
  28   16  0.26
  29   12  0.19
  30   17  0.27
  31   12  0.19

ACGTcount: A:0.41, C:0.02, G:0.24, T:0.34


Consensus pattern (29 bp):   
AAAATGGAATTTTGGAAAATTTGAGGTTA

Found at i:3814 original size:58 final size:57

Alignment explanation


    Indices: 3725--3870  Score: 170
    Period size: 58  Copynumber: 2.5  Consensus size: 57

       3715 CCTTTTGAGG

                 *                           *                * * *      
       3725 AAATGAAATTTTTGGAAGA-TCAGGGGTAAAATGGTAATTTTT-GGAAAATTTGCGGTTAA
          1 AAATGGAA-TTTTGGAA-ATTC-GGGGTAAAATAGT-ATTTTTAGGAAAAATCGAGGTTAA

                               *                                      
       3784 AAATGGAATTTTGGAAATTTGAGGGTAAAATAGTATTTTTAGGAAAAATCGAGGTTAA
          1 AAATGGAATTTTGGAAATTCG-GGGTAAAATAGTATTTTTAGGAAAAATCGAGGTTAA

                            *            
       3842 AAATGGAATTTTGGAAGTTCGGGGTAAAA
          1 AAATGGAATTTTGGAAATTCGGGGTAAAA

       3871 ATGTTATTTT


Statistics
Matches: 76,  Mismatches: 8, Indels: 8
        0.83            0.09        0.09

Matches are distributed among these distances:
  57   16  0.21
  58   53  0.70
  59    7  0.09

ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32


Consensus pattern (57 bp):   
AAATGGAATTTTGGAAATTCGGGGTAAAATAGTATTTTTAGGAAAAATCGAGGTTAA

Done.