Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011240.1 Kokia drynarioides strain JFW-HI SEQ_126218, 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: 2720
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.29

Warning! 83 characters in sequence are not A, C, G, or T


Found at i:738 original size:45 final size:45

Alignment explanation


    Indices: 605--738  Score: 178
    Period size: 45  Copynumber: 3.0  Consensus size: 45

        595 ATAGCTCATC

                                                       * 
        605 AAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACAA
          1 AAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACTA

                                                        *
        650 AAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACTC
          1 AAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACTA

               **           ** * *            *   *     
        695 AAGGGAAGGATATCAGGTTGAGTTTGACGAGCCATCGCGATACT
          1 AAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACT

        739 TTATTCCTCC


Statistics
Matches: 79,  Mismatches: 10, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  45   79  1.00

ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19


Consensus pattern (45 bp):   
AAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATACTA

Found at i:767 original size:21 final size:21

Alignment explanation


    Indices: 734--776  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        724 AGCCATCGCG

                 *  *            
        734 ATACTTTATTCCTCCCGGGCA
          1 ATACTCTACTCCTCCCGGGCA

                           *     
        755 ATACTCTACTCCTCCGGGGCA
          1 ATACTCTACTCCTCCCGGGCA

             
        776 A
          1 A

        777 ATGGACCTTA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28


Consensus pattern (21 bp):   
ATACTCTACTCCTCCCGGGCA

Found at i:1866 original size:17 final size:17

Alignment explanation


    Indices: 1839--1896  Score: 73
    Period size: 17  Copynumber: 3.4  Consensus size: 17

       1829 GGGCCAAATA

                 *           
       1839 AAATTAAAATTTATTTT
          1 AAATTTAAATTTATTTT

                  *        * 
       1856 AAATTTGAATTTATTAT
          1 AAATTTAAATTTATTTT

                              
       1873 AAATTTAAATTTCA-TTT
          1 AAATTTAAATTT-ATTTT

                   
       1890 AAATTTA
          1 AAATTTA

       1897 TNNNNNNNNN


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  17   34  0.97
  18    1  0.03

ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52


Consensus pattern (17 bp):   
AAATTTAAATTTATTTT

Found at i:2051 original size:30 final size:29

Alignment explanation


    Indices: 2017--2086  Score: 95
    Period size: 30  Copynumber: 2.3  Consensus size: 29

       2007 TTTACAAATC

                                        * 
       2017 AAATGGCCCAAATCGACCCAAATACATATT
          1 AAATGGCCCAAAT-GACCCAAATACATACT

                           * *            
       2047 AAATGGCCCAAAATGGCTCAAATACATACT
          1 AAATGGCCC-AAATGACCCAAATACATACT

                      
       2077 AAATGGCCCA
          1 AAATGGCCCA

       2087 TGTCAGCCCA


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  29    1  0.03
  30   31  0.86
  31    4  0.11

ACGTcount: A:0.43, C:0.26, G:0.13, T:0.19


Consensus pattern (29 bp):   
AAATGGCCCAAATGACCCAAATACATACT

Found at i:2677 original size:7 final size:7

Alignment explanation


    Indices: 2645--2686  Score: 50
    Period size: 7  Copynumber: 6.0  Consensus size: 7

       2635 GCCTTTTAAG

                  *
       2645 TTAATAT
          1 TTAATAA

               *   
       2652 TTATTAA
          1 TTAATAA

                    
       2659 TTAATTAA
          1 TTAA-TAA

                   
       2667 -TAATAA
          1 TTAATAA

                   
       2673 TTAATAA
          1 TTAATAA

                   
       2680 TTAATAA
          1 TTAATAA

       2687 ATAAATAAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
   6    3  0.10
   7   24  0.80
   8    3  0.10

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (7 bp):   
TTAATAA

Found at i:2680 original size:21 final size:21

Alignment explanation


    Indices: 2646--2690  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2636 CCTTTTAAGT

                 *   *        *  
       2646 TAATATTTATTAATTAATTAA
          1 TAATAATTAATAATTAATAAA

                                 
       2667 TAATAATTAATAATTAATAAA
          1 TAATAATTAATAATTAATAAA

               
       2688 TAA
          1 TAA

       2691 ATAAAAAGAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (21 bp):   
TAATAATTAATAATTAATAAA
Done.