Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003043.1 Kokia drynarioides strain JFW-HI SEQ_115569, 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, 762

Length: 1270
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.36


Found at i:396 original size:59 final size:59

Alignment explanation


    Indices: 324--770  Score: 628
    Period size: 59  Copynumber: 7.6  Consensus size: 59

        314 GAGGTCCTTA

                           *            *                       *      
        324 AACCTTCCAAAAATTGCCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTAACCCCG
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG

                                       *                *              
        383 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCG
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG

                             *           *    *       *         *     *
        442 AACCTTCCAAAAATTACTATTTTACCCCCAAACTCCCAAAAAACCCATTTTTAACCCCA
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG

                                         *                *          *  
        501 AACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAAGTCCTATTTTTGACCTCG
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAA-TCCCATTTTTGACCCCG

                                       *                          *      
        561 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAAGTCCCATTTTTTTACCCCG
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAA-TCCCA-TTTTTGACCCCG

             *            * *                        *                *
        622 AGCCTTCCAAAAATGAACATTTTACCCCCGAACTTCCAAAAGTCCCATTTTT-ACCCCA
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG

                                       *                     *       * 
        680 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTCTTGACCCTG
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG

                            *                
        739 AACCTTCC-AAAATTAACATTTTACCCCCGAAC
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAAC

        771 GTTTGAAATT


Statistics
Matches: 344,  Mismatches: 41, Indels: 7
        0.88            0.10        0.02

Matches are distributed among these distances:
  58   73  0.21
  59  162  0.47
  60   62  0.18
  61   47  0.14

ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28


Consensus pattern (59 bp):   
AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG

Found at i:751 original size:29 final size:29

Alignment explanation


    Indices: 324--770  Score: 385
    Period size: 29  Copynumber: 15.1  Consensus size: 29

        314 GAGGTCCTTA

                           *              
        324 AACCTTCCAAAAATTGCCATTTTACCCCTG
          1 AACCTTCCAAAAATTCCCATTTTACCCC-G

                                           
        354 AA-CTTCCAAAAA-TCCCATTTTTAACCCCG
          1 AACCTTCCAAAAATTCCCA-TTTT-ACCCCG

                           *              
        383 AACCTTCCAAAAATTACCATTTTACCCTCG
          1 AACCTTCCAAAAATTCCCATTTTACCC-CG

                            *              
        413 AA-CTTCCAAAAA-TCTCATTTTTGACCCCG
          1 AACCTTCCAAAAATTCCCA-TTTT-ACCCCG

                           * *          *
        442 AACCTTCCAAAAATTACTATTTTACCCCC
          1 AACCTTCCAAAAATTCCCATTTTACCCCG

              *  *        *               *
        471 AAACTCCCAAAAA-ACCCATTTTTAACCCCA
          1 AACCTTCCAAAAATTCCCA-TTTT-ACCCCG

                           *            *
        501 AACCTTCCAAAAATTACCATTTTACCCCC
          1 AACCTTCCAAAAATTCCCATTTTACCCCG

              *          *   *          *  
        530 AAACTTCCAAAAAGTCCTATTTTTGACCTCG
          1 AACCTTCCAAAAATTCCCA-TTTT-ACCCCG

                           *              
        561 AACCTTCCAAAAATTACCATTTTACCCTCG
          1 AACCTTCCAAAAATTCCCATTTTACCC-CG

                         *                  
        591 AA-CTTCCAAAAAGTCCCATTTTTTTACCCCG
          1 AACCTTCCAAAAATTCCCA---TTTTACCCCG

             *            ***             
        622 AGCCTTCCAAAAATGAACATTTTACCCCCG
          1 AACCTTCCAAAAATTCCCATTTTA-CCCCG

                         *               *
        652 AA-CTTCC-AAAAGTCCCATTTTTACCCCA
          1 AACCTTCCAAAAATTCCCA-TTTTACCCCG

                           *              
        680 AACCTTCCAAAAATTACCATTTTACCCTCG
          1 AACCTTCCAAAAATTCCCATTTTACCC-CG

                                         * 
        710 AA-CTTCCAAAAA-TCCCATTCTTGACCCTG
          1 AACCTTCCAAAAATTCCCATT-TT-ACCCCG

                           **             
        739 AACCTTCC-AAAATTAACATTTTACCCCCG
          1 AACCTTCCAAAAATTCCCATTTTA-CCCCG

               
        768 AAC
          1 AAC

        771 GTTTGAAATT


Statistics
Matches: 337,  Mismatches: 51, Indels: 59
        0.75            0.11        0.13

Matches are distributed among these distances:
  28   28  0.08
  29  152  0.45
  30  106  0.31
  31   31  0.09
  32   20  0.06

ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28


Consensus pattern (29 bp):   
AACCTTCCAAAAATTCCCATTTTACCCCG
Done.