Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012651.1 Kokia drynarioides strain JFW-HI SEQ_127662, 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: 3345
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34


Found at i:116 original size:38 final size:38

Alignment explanation


    Indices: 73--180  Score: 147
    Period size: 32  Copynumber: 3.0  Consensus size: 38

         63 ACATATTCAA

                     *                            
         73 ATATCATATTAGAATATCATATTTCTAGAAACATATAT
          1 ATATCATATCAGAATATCATATTTCTAGAAACATATAT

                       *   *                      
        111 ATATCATATCAAAATGTCATATTTCTAG----A-A-AT
          1 ATATCATATCAGAATATCATATTTCTAGAAACATATAT

                                                  
        143 ATATCATATCAGAATATCATATTTCTAGAAACATATAT
          1 ATATCATATCAGAATATCATATTTCTAGAAACATATAT

        181 CAGGTTAAAA


Statistics
Matches: 59,  Mismatches: 5, Indels: 12
        0.78            0.07        0.16

Matches are distributed among these distances:
  32   28  0.47
  33    1  0.02
  34    1  0.02
  36    1  0.02
  37    1  0.02
  38   27  0.46

ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38


Consensus pattern (38 bp):   
ATATCATATCAGAATATCATATTTCTAGAAACATATAT

Found at i:180 original size:16 final size:16

Alignment explanation


    Indices: 129--180  Score: 54
    Period size: 16  Copynumber: 3.2  Consensus size: 16

        119 TCAAAATGTC

                            
        129 ATATTTCTAGAAATAT
          1 ATATTTCTAGAAATAT

                 *           
        145 ATCATATC-AG-AATAT
          1 AT-ATTTCTAGAAATAT

                          *  
        160 CATATTTCTAGAAACAT
          1 -ATATTTCTAGAAATAT

                
        177 ATAT
          1 ATAT

        181 CAGGTTAAAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 8
        0.73            0.08        0.20

Matches are distributed among these distances:
  15    9  0.31
  16   12  0.41
  17    8  0.28

ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38


Consensus pattern (16 bp):   
ATATTTCTAGAAATAT

Found at i:197 original size:34 final size:34

Alignment explanation


    Indices: 73--198  Score: 130
    Period size: 32  Copynumber: 3.6  Consensus size: 34

         63 ACATATTCAA

                     * *   *                      
         73 ATATCATATTAGAATATCATATTTCTAGAAACATATAT
          1 ATATCATATCAAAATGTCATATTTCTAGAAAC----AT

                                              
        111 ATATCATATCAAAATGTCATATTTCTAG-AA-AT
          1 ATATCATATCAAAATGTCATATTTCTAGAAACAT

                       *   *                  
        143 ATATCATATCAGAATATCATATTTCTAGAAACAT
          1 ATATCATATCAAAATGTCATATTTCTAGAAACAT

                  ** *            
        177 ATATCAGGTTAAAATGTCATAT
          1 ATATCATATCAAAATGTCATAT

        199 CAAATCGGAA


Statistics
Matches: 76,  Mismatches: 10, Indels: 8
        0.81            0.11        0.09

Matches are distributed among these distances:
  32   28  0.37
  33    2  0.03
  34   19  0.25
  37    2  0.03
  38   25  0.33

ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37


Consensus pattern (34 bp):   
ATATCATATCAAAATGTCATATTTCTAGAAACAT
Done.