Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002834.1 Kokia drynarioides strain JFW-HI SEQ_115207, 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: 3524
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38


Found at i:589 original size:30 final size:30

Alignment explanation


    Indices: 526--870  Score: 354
    Period size: 29  Copynumber: 11.7  Consensus size: 30

        516 GTCCCTAAAC

                          *      *        
        526 CTTCCAAAAATTCCGTTTTTACCCCCG-AA
          1 CTTCCAAAAATTCCATTTTTAACCCCGAAA

                        *           *     
        555 CTTCCAAAAATTTCATTTTTAACCTCGAAA
          1 CTTCCAAAAATTCCATTTTTAACCCCGAAA

                         *           *  *  
        585 CTTCCAAAAATTCTATTTTT-ACTCTC-TAA
          1 CTTCCAAAAATTCCATTTTTAAC-CCCGAAA

                                     **   
        614 CTTCCAAAAATTCCA-TTTTAACCCTAAAA
          1 CTTCCAAAAATTCCATTTTTAACCCCGAAA

                                 *     *   
        643 CTTCCAAAAA-TCCTATTTTTGACCCCAAAA
          1 CTTCCAAAAATTCC-ATTTTTAACCCCGAAA

                *                          
        673 CTTCTAAAAATTCCATTTTT-ACTCCCG-AA
          1 CTTCCAAAAATTCCATTTTTAAC-CCCGAAA

                       *         *  *      
        702 CTTCCAAAAATCCCATTCTTTGACTCCGAAA
          1 CTTCCAAAAATTCCATT-TTTAACCCCGAAA

                         *                 
        733 CTTCCAAAAATTCTATTTTT-ACCCTCG-AA
          1 CTTCCAAAAATTCCATTTTTAACCC-CGAAA

                       *        *     *   
        762 CTTCCAAAAATCCCATTTTTGACCCCAAAA
          1 CTTCCAAAAATTCCATTTTTAACCCCGAAA

                                           
        792 CTTCCAAAAATTCCATTTTT-ACCCCTG-AA
          1 CTTCCAAAAATTCCATTTTTAACCCC-GAAA

                                 *         
        821 CTTCCAAAAA-TCTCATTTTTGACCCCGAAA
          1 CTTCCAAAAATTC-CATTTTTAACCCCGAAA

                *               
        851 CTTCTAAAAATTCCATTTTT
          1 CTTCCAAAAATTCCATTTTT

        871 TCCCTTAACC


Statistics
Matches: 270,  Mismatches: 27, Indels: 37
        0.81            0.08        0.11

Matches are distributed among these distances:
  28   10  0.04
  29  124  0.46
  30  112  0.41
  31   24  0.09

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


Consensus pattern (30 bp):   
CTTCCAAAAATTCCATTTTTAACCCCGAAA

Found at i:618 original size:59 final size:59

Alignment explanation


    Indices: 526--988  Score: 412
    Period size: 59  Copynumber: 7.8  Consensus size: 59

        516 GTCCCTAAAC

                       *  *           **              *           *     
        526 CTTCCAAAAATTCCGTTTTT-ACCCCCGAACTTCCAAAAATTTCATTTTTAACCTCGAAA
          1 CTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCCG-AA

                       * *           *  *                            **  
        585 CTTCCAAAAATTCTATTTTT-ACTCTC-TAACTTCCAAAAATTCCA-TTTTAACCCTAAAA
          1 CTTCCAAAAATCCCATTTTTGAC-CCCAAAACTTCCAAAAATTCCATTTTTAACCC-CGAA

                         *                    *                         
        643 CTTCCAAAAATCCTATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTT-ACTCCCGAA
          1 CTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAAC-CCCGAA

                                    *  *                *                
        702 CTTCCAAAAATCCCATTCTTTGACTCCGAAACTTCCAAAAATTCTATTTTT-ACCCTCGAA
          1 CTTCCAAAAATCCCATT-TTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCC-CGAA

                                                                        
        762 CTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTT-ACCCCTGAA
          1 CTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCC-GAA

                        *             *       *                *   **  
        821 CTTCCAAAAATCTCATTTTTGACCCCGAAACTTCTAAAAATTCCATTTTT-TCCCTTAA
          1 CTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCCGAA

             *                 **    *                     *           *   
        879 CCTCC-AAAATCTCCATTTCCGACCTCAAAAC-TCTC-AAAATTACCCTTTTT-ACTCCTGAA
          1 CTTCCAAAAATC-CCATTTTTGACCCCAAAACTTC-CAAAAATT-CCATTTTTAAC-CCCGAA

                        *         *         *    *              
        938 -TGTCCAAAAATTCCATTTTTAAACCCCAAAATTTCCCAAAATTACCATTTT
          1 CT-TCCAAAAATCCCATTTTT-GACCCCAAAACTTCCAAAAATT-CCATTTT

        989 GCCCCTAGGT


Statistics
Matches: 340,  Mismatches: 46, Indels: 34
        0.81            0.11        0.08

Matches are distributed among these distances:
  57   14  0.04
  58   60  0.18
  59  177  0.52
  60   74  0.22
  61   15  0.04

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


Consensus pattern (59 bp):   
CTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCCCGAA
Done.