Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007665.1 Kokia drynarioides strain JFW-HI SEQ_122296, 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: 10441
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36


Found at i:4681 original size:31 final size:31

Alignment explanation


    Indices: 4643--4702  Score: 111
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       4633 CCGAGCCTCA

                                *          
       4643 AGTAAGGCACTGTTCACTCGGGCTCAGCTCG
          1 AGTAAGGCACTGTTCACTCGAGCTCAGCTCG

                                         
       4674 AGTAAGGCACTGTTCACTCGAGCTCAGCT
          1 AGTAAGGCACTGTTCACTCGAGCTCAGCT

       4703 TGAAATCAAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.22, C:0.28, G:0.27, T:0.23


Consensus pattern (31 bp):   
AGTAAGGCACTGTTCACTCGAGCTCAGCTCG

Found at i:4697 original size:26 final size:26

Alignment explanation


    Indices: 4634--4699  Score: 69
    Period size: 31  Copynumber: 2.3  Consensus size: 26

       4624 CGAGCCGAGC

                                       
       4634 CGAGCCTCAAGTAAGGCACTGTTCACT
          1 CGAG-CTCAAGTAAGGCACTGTTCACT

                        *                  
       4661 CGGGCTCAGCTCGAGTAAGGCACTGTTCACT
          1 C--G---AGCTCAAGTAAGGCACTGTTCACT

                    
       4692 CGAGCTCA
          1 CGAGCTCA

       4700 GCTTGAAATC


Statistics
Matches: 32,  Mismatches: 2, Indels: 11
        0.71            0.04        0.24

Matches are distributed among these distances:
  26    5  0.16
  27    1  0.03
  29    2  0.06
  31   22  0.69
  32    2  0.06

ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21


Consensus pattern (26 bp):   
CGAGCTCAAGTAAGGCACTGTTCACT

Found at i:4848 original size:40 final size:41

Alignment explanation


    Indices: 4801--4908  Score: 125
    Period size: 40  Copynumber: 2.7  Consensus size: 41

       4791 TTTGGGCAGA

                               *                  *   
       4801 AAACGCCGTAAAAAGTAAATCAATAGCGA-C-ATTTTTCCAT
          1 AAACGCCGTAAAAAGTAAAGCAATAGCGAGCGA-TTTTACAT

                          *                           
       4841 AAACGCCGCT-AAAGGTAAAGCAATAGC-AGCGATTTTACAT
          1 AAACGCCG-TAAAAAGTAAAGCAATAGCGAGCGATTTTACAT

                    *    *              
       4881 AAACGCCGCAAAATGTAAAGCAATAGCG
          1 AAACGCCGTAAAAAGTAAAGCAATAGCG

       4909 GTGTTTGTAG


Statistics
Matches: 58,  Mismatches: 5, Indels: 9
        0.81            0.07        0.12

Matches are distributed among these distances:
  39    1  0.02
  40   55  0.95
  41    2  0.03

ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19


Consensus pattern (41 bp):   
AAACGCCGTAAAAAGTAAAGCAATAGCGAGCGATTTTACAT

Found at i:6837 original size:41 final size:41

Alignment explanation


    Indices: 6731--6839  Score: 130
    Period size: 41  Copynumber: 2.7  Consensus size: 41

       6721 TTTTTAAAAA

                   *             * *      *          
       6731 ATTAAAATTCAAGCAATAGCGACATTTATGGGAAAAACACC
          1 ATTAAAAGTCAAGCAATAGCGGCGTTTATGAGAAAAACACC

             *                 *                  *   
       6772 ACTAAAAGTCAAGCAATAGTGGCGTTTATGAGAAAAATGA-C
          1 ATTAAAAGTCAAGCAATAGCGGCGTTTATGAGAAAAA-CACC

                          *            
       6813 ATTAAAAGTCAAGCGATAGCGGCGTTT
          1 ATTAAAAGTCAAGCAATAGCGGCGTTT

       6840 TCCTATAAAT


Statistics
Matches: 57,  Mismatches: 10, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  41   56  0.98
  42    1  0.02

ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23


Consensus pattern (41 bp):   
ATTAAAAGTCAAGCAATAGCGGCGTTTATGAGAAAAACACC

Found at i:7155 original size:18 final size:18

Alignment explanation


    Indices: 7121--7168  Score: 69
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       7111 CTTATCAAAA

                      *        
       7121 AAATTCCTCATTCATTTCT
          1 AAATTCCT-AATCATTTCT

                              
       7140 AAATTCCTAATCATTTCT
          1 AAATTCCTAATCATTTCT

                *      
       7158 AAATCCCTAAT
          1 AAATTCCTAAT

       7169 TTCCACCAAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  18   19  0.70
  19    8  0.30

ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42


Consensus pattern (18 bp):   
AAATTCCTAATCATTTCT
Done.