Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008065.1 Kokia drynarioides strain JFW-HI SEQ_122721, 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: 8993
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:8547 original size:23 final size:23

Alignment explanation


    Indices: 8411--8558  Score: 106
    Period size: 23  Copynumber: 6.3  Consensus size: 23

       8401 ACAAAGTACT

                               *   
       8411 GAGCACACAAAGTGCTAATTAGA
          1 GAGCACACAAAGTGCTAATCAGA

                    *          *     
       8434 GAGCACACGAAGTGCTAATAATGGA
          1 GAGCACACAAAGTGCTAATCA--GA

                            *   **   
       8459 GAGCACGA-AACA-TGTTAAAAAGA
          1 GAGCAC-ACAA-AGTGCTAATCAGA

                       *      *     
       8482 GAGCACACAAAATGCTAAAC-GAA
          1 GAGCACACAAAGTGCTAATCAG-A

            *  *         *         
       8505 AAGTACACAAAGTACTAATCAGA
          1 GAGCACACAAAGTGCTAATCAGA

                     *              
       8528 GAGCACACACAGTGCTAATC-GAA
          1 GAGCACACAAAGTGCTAATCAG-A

                    
       8551 GAGCACAC
          1 GAGCACAC

       8559 GCAATGCTAA


Statistics
Matches: 100,  Mismatches: 16, Indels: 18
        0.75            0.12        0.13

Matches are distributed among these distances:
  22    4  0.04
  23   77  0.77
  24    1  0.01
  25   16  0.16
  26    2  0.02

ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14


Consensus pattern (23 bp):   
GAGCACACAAAGTGCTAATCAGA

Found at i:8566 original size:23 final size:23

Alignment explanation


    Indices: 8481--8577  Score: 81
    Period size: 23  Copynumber: 4.2  Consensus size: 23

       8471 TGTTAAAAAG

                      *        *   
       8481 AGAGCACACAAAATGCTAAACGA
          1 AGAGCACACACAATGCTAATCGA

             *  *          *        
       8504 AAAGTACACA-AAGTACTAATC-A
          1 AGAGCACACACAA-TGCTAATCGA

                         *          
       8526 GAGAGCACACACAGTGCTAATCGA
          1 -AGAGCACACACAATGCTAATCGA

                     *         *  *
       8550 AGAGCACACGCAATGCTAACCGG
          1 AGAGCACACACAATGCTAATCGA

                 
       8573 AGAGC
          1 AGAGC

       8578 GCTAGTATTC


Statistics
Matches: 58,  Mismatches: 12, Indels: 8
        0.74            0.15        0.10

Matches are distributed among these distances:
  22    3  0.05
  23   53  0.91
  24    2  0.03

ACGTcount: A:0.44, C:0.24, G:0.21, T:0.11


Consensus pattern (23 bp):   
AGAGCACACACAATGCTAATCGA

Found at i:8741 original size:20 final size:23

Alignment explanation


    Indices: 8703--8747  Score: 69
    Period size: 20  Copynumber: 2.1  Consensus size: 23

       8693 AAACACAAAC

                                   
       8703 ATATCATCATGTATATATCACAT
          1 ATATCATCATGTATATATCACAT

                                   
       8726 ATATCATCAT-T-T-TATCACAT
          1 ATATCATCATGTATATATCACAT

              
       8746 AT
          1 AT

       8748 TTAACATCAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  20   10  0.45
  21    1  0.05
  22    1  0.05
  23   10  0.45

ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42


Consensus pattern (23 bp):   
ATATCATCATGTATATATCACAT
Done.