Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009230.1 Kokia drynarioides strain JFW-HI SEQ_123935, 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: 2409
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36


Found at i:529 original size:30 final size:29

Alignment explanation


    Indices: 466--975  Score: 455
    Period size: 29  Copynumber: 17.3  Consensus size: 29

        456 GTCCTTAAAC

                *       *          **     
        466 CTTCGAAAAATTTCATTTTTATCTATG-AA
          1 CTTCCAAAAATTCCATTTTTA-CCCTGAAA

                       *                  
        495 CTTCCAAAAATCCCATTTTTGACCCTGAAA
          1 CTTCCAAAAATTCCATTTTT-ACCCTGAAA

                         *       *   *    
        525 CTTCCAAAAATTCTATTTTTTTCCCCG-AA
          1 CTTCCAAAAATTCCA-TTTTTACCCTGAAA

                                     **   
        554 CTTCCAAAAATTCCATTTTTAACCCCAAAA
          1 CTTCCAAAAATTCCATTTTT-ACCCTGAAA

                  *    *       *      *   
        584 CTTCCACAAATCCCATTTTGA-CCTCAAAA
          1 CTTCCAAAAATTCCATTTTTACCCT-GAAA

                      *                *   
        613 CTTCC-AAAACTCTCATTTTTAACCCTAAAA
          1 CTTCCAAAAATTC-CATTTTT-ACCCTGAAA

                         *           *   
        643 CTTCCAAAAATTCTATTTTTACCCTCAAA
          1 CTTCCAAAAATTCCATTTTTACCCTGAAA

                *      *         *        
        672 CTTCTAAAAATCCCATTTTTAACCTCGAAA
          1 CTTCCAAAAATTCCATTTTTACCCT-GAAA

                     *              **   
        702 CTTCCAAAATTTCCATTTTTACCCCCAAA
          1 CTTCCAAAAATTCCATTTTTACCCTGAAA

                                       **   
        731 CTTCCAAAAA-TCTCATTTTTTTACCCCAAAA
          1 CTTCCAAAAATTC-CA--TTTTTACCCTGAAA

                                          
        762 CTTCCAAAAATTCCATTTTTACCCCT-AAA
          1 CTTCCAAAAATTCCATTTTTA-CCCTGAAA

            *         **                  
        791 TTTCCAAAAACCCCATTTTTGACCCTGAAA
          1 CTTCCAAAAATTCCATTTTT-ACCCTGAAA

               *                     *    
        821 CTTTCAAAAATTCCATTTTTACTCCCG-AA
          1 CTTCCAAAAATTCCATTTTTAC-CCTGAAA

                       *       *     *   
        850 CTTCCAAAAATCCCATTTTGACCCTAAAA
          1 CTTCCAAAAATTCCATTTTTACCCTGAAA

                                          
        879 CTTCCAAAAATTCCATTTTTACCCTCG-AA
          1 CTTCCAAAAATTCCATTTTTACCCT-GAAA

                       *              *    
        908 CTTCCAAAAATGCCATTTTTGACCCCCGAAA
          1 CTTCCAAAAATTCCATTTTT-A-CCCTGAAA

                                *         
        939 CTTCCAAAAATTCCA-TTTTGCCCTCG-AA
          1 CTTCCAAAAATTCCATTTTTACCCT-GAAA

                     
        967 CTTCCAAAA
          1 CTTCCAAAA

        976 TCTTCATATT


Statistics
Matches: 398,  Mismatches: 58, Indels: 51
        0.79            0.11        0.10

Matches are distributed among these distances:
  28   29  0.07
  29  199  0.50
  30  110  0.28
  31   58  0.15
  32    2  0.01

ACGTcount: A:0.34, C:0.29, G:0.03, T:0.33


Consensus pattern (29 bp):   
CTTCCAAAAATTCCATTTTTACCCTGAAA

Found at i:563 original size:59 final size:58

Alignment explanation


    Indices: 492--975  Score: 551
    Period size: 59  Copynumber: 8.2  Consensus size: 58

        482 TTTTATCTAT

                                         *                *       *    
        492 GAACTTCCAAAAATCCCATTTTTGACCCTGAAACTTCCAAAAATTCTATTTTTTTCCCC
          1 GAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCA-TTTTTACCCC

                          *        *    *          *    *       *     *
        551 GAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCACAAATCCCATTTTGACCTCA
          1 GAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACC-CC

            *           *  *       *                      *            
        610 AAACTTCCAAAACTCTCATTTTTAACCCTAAAACTTCCAAAAATTCTATTTTTACCCTC
          1 GAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCC-C

            *      *                 *    *            *                
        669 AAACTTCTAAAAATCCCATTTTT-AACCTCGAAACTTCCAAAATTTCCATTTTTACCCCC
          1 GAACTTCCAAAAATCCCATTTTTGACCCT-AAAACTTCCAAAAATTCCATTTTTA-CCCC

            *              *        *    *                             
        728 AAACTTCCAAAAATCTCATTTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCC
          1 GAACTTCCAAAAATCCCA-TTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCC

             *  *         *               *      *                      
        787 TAAATTTCCAAAAACCCCATTTTTGACCCTGAAACTTTCAAAAATTCCATTTTTACTCCC
          1 -GAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTAC-CCC

                                                                       
        847 GAACTTCCAAAAATCCCA-TTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCTC
          1 GAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCC-C

                          *              **                       *     
        905 GAACTTCCAAAAATGCCATTTTTGACCCCCGAAACTTCCAAAAATTCCA-TTTTGCCCTC
          1 GAACTTCCAAAAATCCCATTTTTGA-CCCTAAAACTTCCAAAAATTCCATTTTTACCC-C

                        
        964 GAACTTCCAAAA
          1 GAACTTCCAAAA

        976 TCTTCATATT


Statistics
Matches: 365,  Mismatches: 49, Indels: 22
        0.84            0.11        0.05

Matches are distributed among these distances:
  57    2  0.01
  58   63  0.17
  59  227  0.62
  60   70  0.19
  61    3  0.01

ACGTcount: A:0.34, C:0.30, G:0.03, T:0.32


Consensus pattern (58 bp):   
GAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCC
Done.