Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010167.1 Kokia drynarioides strain JFW-HI SEQ_124972, 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: 2431
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35


Found at i:632 original size:29 final size:29

Alignment explanation


    Indices: 598--1048  Score: 336
    Period size: 29  Copynumber: 15.4  Consensus size: 29

        588 GTCCCTAAAC

                                         
        598 CTTCCAAAAATTACCATTTTACCCCCGAA
          1 CTTCCAAAAATTACCATTTTACCCCCGAA

                        *                  
        627 CTTCCAAAAA-TCCCATTTTTGA-CCCCGAA
          1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA

                 *         *          *   
        656 TCTTCAAAAAATTACTATTTTACCCCTGAA
          1 -CTTCCAAAAATTACCATTTTACCCCCGAA

                * *                      *  
        686 CTTCTAGAAA-T-CCAATTTTTGA-CCCCAAA
          1 CTTCCAAAAATTACC-A-TTTT-ACCCCCGAA

                           *           *  
        715 TCTTCCAAAAATTACTATTTTACCCCCAAA
          1 -CTTCCAAAAATTACCATTTTACCCCCGAA

                        *           *     
        745 CTTCCAAAAA-TCCCATTTTGA-CACCGAA
          1 CTTCCAAAAATTACCATTTT-ACCCCCGAA

                           *              
        773 TCTTCCAAAAATTACTATTTTA-CCCCGAA
          1 -CTTCCAAAAATTACCATTTTACCCCCGAA

                        *              *  *
        802 CTTCCAAAAA-TCCCATTTTTAACCCCGGAC
          1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA

                *                    *   
        832 CTTCTAAAAATTACCATTTTACCCCTGAA
          1 CTTCCAAAAATTACCATTTTACCCCCGAA

                        *         *  *    
        861 CTTCCAAAAA-TCCCATTTTTAACCTCGAA
          1 CTTCCAAAAATTACCA-TTTTACCCCCGAA

                 **                    *  
        890 CCTTCTTAAAATTACCATTTTACCCCCAAA
          1 -CTTCCAAAAATTACCATTTTACCCCCGAA

                      * *             **   
        920 CTTCC-AAAAGTCCCATTTTTGA-CCTTGAA
          1 CTTCCAAAAATTACCA-TTTT-ACCCCCGAA

                           *     *        
        949 TCTTCCAAAAATTACTATTTTCCCCCCGAA
          1 -CTTCCAAAAATTACCATTTTACCCCCGAA

                         *         *   *   
        979 -TTCCCAAAAA-TCCCATTTTTAGCCCTGAA
          1 CTT-CCAAAAATTACCA-TTTTACCCCCGAA

                                     *    
       1008 TCTTCCAAAAATTACCATTTTACCCTCGAA
          1 -CTTCCAAAAATTACCATTTTACCCCCGAA

                       
       1038 CTTCCAAAAAT
          1 CTTCCAAAAAT

       1049 CCTATTTTTG


Statistics
Matches: 330,  Mismatches: 60, Indels: 64
        0.73            0.13        0.14

Matches are distributed among these distances:
  27    4  0.01
  28   49  0.15
  29  135  0.41
  30  115  0.35
  31   26  0.08
  32    1  0.00

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


Consensus pattern (29 bp):   
CTTCCAAAAATTACCATTTTACCCCCGAA

Found at i:697 original size:59 final size:59

Alignment explanation


    Indices: 598--1084  Score: 608
    Period size: 59  Copynumber: 8.3  Consensus size: 59

        588 GTCCCTAAAC

                                                                       
        598 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
          1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT

                *         *          *       * *      *            *   
        657 CTTCAAAAAATTACTATTTTACCCCTGAACTTCTAGAAATCCAATTTTTGACCCCAAAT
          1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT

                          *           *                         *      
        716 CTTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTGACACCGAAT
          1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT

                          *                                  *      * *
        774 CTTCCAAAAATTACTATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTAACCCCGGAC
          1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT

                *                    *                       *   *    *
        832 CTTCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCTCGAAC
          1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT

                **                    *           *              **    
        891 CTTCTTAAAATTACCATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTGACCTTGAAT
          1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT

                          *     *                                   *    
        950 CTTCCAAAAATTACTATTTTCCCCCCGAA-TTCCCAAAAATCCCATTTTT-AGCCCTGAAT
          1 CTTCCAAAAATTACCATTTTACCCCCGAACTT-CCAAAAATCCCATTTTTGA-CCCCGAAT

                                    *                 *        **      
       1009 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTTGATTCCGAA-
          1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT

                       *       
       1067 CATTCC-AAAACTACCATT
          1 C-TTCCAAAAATTACCATT

       1085 CTGCCACTCC


Statistics
Matches: 374,  Mismatches: 47, Indels: 15
        0.86            0.11        0.03

Matches are distributed among these distances:
  57   21  0.06
  58   77  0.21
  59  273  0.73
  60    3  0.01

ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32


Consensus pattern (59 bp):   
CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT

Done.