Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005555.1 Kokia drynarioides strain JFW-HI SEQ_119662, 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, 924

Length: 1541
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33


Found at i:786 original size:29 final size:29

Alignment explanation


    Indices: 751--937  Score: 141
    Period size: 29  Copynumber: 6.3  Consensus size: 29

        741 CCCCAGATTG

                      *                   
        751 TCCAAAAA-TCCCATTTTAACCCCGAATCT
          1 TCCAAAAATTACCATTTTAACCCCGAA-CT

             **         *      *         
        780 TTTAAAAATTACAATTTTACCCCCGAACT
          1 TCCAAAAATTACCATTTTAACCCCGAACT

                      *         *     *     
        809 TCCAAAAA-TCCCATTTTTTGACCCCAAACCT
          1 TCCAAAAATTACCA--TTTTAACCCCGAA-CT

                                          
        840 TCCAAAAATTACCATTTT-ACCCTCGAACT
          1 TCCAAAAATTACCATTTTAACCC-CGAACT

                      *          *          
        869 TCCAAAAA-TCCCATTTTTGACCCCCGAACCT
          1 TCCAAAAATTACCA-TTTT-AACCCCGAA-CT

             *                      **    
        900 TTCAAAAATTACCATTTT-ACCCTTAAACT
          1 TCCAAAAATTACCATTTTAACCC-CGAACT

                     
        929 TCCAAAAAT
          1 TCCAAAAAT

        938 CTCATTTTTG


Statistics
Matches: 124,  Mismatches: 22, Indels: 24
        0.73            0.13        0.14

Matches are distributed among these distances:
  28    7  0.06
  29   45  0.36
  30   38  0.31
  31   26  0.21
  32    8  0.06

ACGTcount: A:0.35, C:0.31, G:0.03, T:0.30


Consensus pattern (29 bp):   
TCCAAAAATTACCATTTTAACCCCGAACT

Found at i:804 original size:30 final size:29

Alignment explanation


    Indices: 763--979  Score: 136
    Period size: 29  Copynumber: 7.3  Consensus size: 29

        753 CAAAAATCCC

                  *           **          
        763 ATTTTAACCCCGAATCTTTTAAAAATTACA
          1 ATTTTACCCCCGAA-CTTCCAAAAATTACA

                                     **  
        793 ATTTTACCCCCGAACTTCCAAAAATCCCA
          1 ATTTTACCCCCGAACTTCCAAAAATTACA

             *           *                 *
        822 TTTTTTGA-CCCCAAACCTTCCAAAAATTACC
          1 -ATTTT-ACCCCCGAA-CTTCCAAAAATTACA

                     *               **  
        853 ATTTTACCCTCGAACTTCCAAAAATCCCA
          1 ATTTTACCCCCGAACTTCCAAAAATTACA

            *                  *          *
        882 TTTTTGACCCCCGAACCTTTCAAAAATTACC
          1 ATTTT-ACCCCCGAA-CTTCCAAAAATTACA

                     ***                  
        913 ATTTTACCCTTAAACTTCCAAAAATCT-CA
          1 ATTTTACCCCCGAACTTCCAAAAAT-TACA

            *        *                *   *
        942 TTTTTGA-CTCCGAACCTTCC-AAAACTACT
          1 ATTTT-ACCCCCGAA-CTTCCAAAAATTACA

                     
        971 ATTTTACCC
          1 ATTTTACCC

        980 TCGTGCATTC


Statistics
Matches: 139,  Mismatches: 37, Indels: 23
        0.70            0.19        0.12

Matches are distributed among these distances:
  28    2  0.01
  29   56  0.40
  30   53  0.38
  31   28  0.20

ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32


Consensus pattern (29 bp):   
ATTTTACCCCCGAACTTCCAAAAATTACA

Found at i:849 original size:60 final size:59

Alignment explanation


    Indices: 751--982  Score: 306
    Period size: 60  Copynumber: 3.9  Consensus size: 59

        741 CCCCAGATTG

                              *        *   **         *         *      
        751 TCCAAAAATCCCA-TTTTAACCCCGAATCTTTTAAAAATTACAATTTTACCCCCGAACT
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACT

                                     *                                  
        809 TCCAAAAATCCCATTTTTTGACCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAACT
          1 TCCAAAAATCCCA-TTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACT

                                            *                     **    
        869 TCCAAAAATCCCATTTTTGACCCCCGAACCTTTCAAAAATTACCATTTTACCCTTAAACT
          1 TCCAAAAATCCCATTTTTGA-CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACT

                      *          *                *   *            
        929 TCCAAAAATCTCATTTTTGACTCCGAACCTTCC-AAAACTACTATTTTACCCTCG
          1 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCG

        983 TGCATTCGAA


Statistics
Matches: 153,  Mismatches: 18, Indels: 6
        0.86            0.10        0.03

Matches are distributed among these distances:
  58   30  0.20
  59   18  0.12
  60  105  0.69

ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31


Consensus pattern (59 bp):   
TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACT

Done.