Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000635.1 Kokia drynarioides strain JFW-HI SEQ_111598, 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, 868

Length: 1447
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37


Found at i:497 original size:29 final size:29

Alignment explanation


    Indices: 449--736  Score: 278
    Period size: 29  Copynumber: 9.7  Consensus size: 29

        439 GACGTCCTTG

                                          
        449 AACTGTCCAAAAATTCCATTTTTACCCCCA
          1 AACT-TCCAAAAATTCCATTTTTACCCCCA

                                         * 
        479 AACTTCCAAAAA-TCTCATTTTTGACCCCAA
          1 AACTTCCAAAAATTC-CATTTTT-ACCCCCA

                 *           **       * *
        509 AACTTTCAAAAATTCCAAATTTACCCTCG
          1 AACTTCCAAAAATTCCATTTTTACCCCCA

                         *              * 
        538 AACTTCCAAAAATCCCATTTTTAACCCCAA
          1 AACTTCCAAAAATTCCATTTTT-ACCCCCA

                           *              * 
        568 AACTTCCAAAAATT-TAGTTTTTCGACCCCGA
          1 AACTTCCAAAAATTCCA-TTTTT--ACCCCCA

                                *     * *
        599 AACTTCCAAAAATTCCATTTCTACCCTCG
          1 AACTTCCAAAAATTCCATTTTTACCCCCA

                             *           
        628 AACTTCCAAAAATTCCAATTTTACCCCCA
          1 AACTTCCAAAAATTCCATTTTTACCCCCA

                         *              * 
        657 AACTTCCAAAAATGCCATTTTTGACCCCAA
          1 AACTTCCAAAAATTCCATTTTT-ACCCCCA

                  *                    * *
        687 AACTT-TACAAAATTCCATTTTTACCCTCG
          1 AACTTCCA-AAAATTCCATTTTTACCCCCA

               *                  
        716 AACCTCC-AAAATCTCCATTTT
          1 AACTTCCAAAAAT-TCCATTTT

        737 CGACCTCGAA


Statistics
Matches: 210,  Mismatches: 37, Indels: 23
        0.78            0.14        0.09

Matches are distributed among these distances:
  28    7  0.03
  29  104  0.50
  30   72  0.34
  31   26  0.12
  32    1  0.00

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


Consensus pattern (29 bp):   
AACTTCCAAAAATTCCATTTTTACCCCCA

Found at i:548 original size:59 final size:59

Alignment explanation


    Indices: 449--771  Score: 297
    Period size: 59  Copynumber: 5.5  Consensus size: 59

        439 GACGTCCTTG

                                         *                              
        449 AACTGTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAA
          1 AACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCAA

                 *           **       *                *       *       
        509 AACTTTCAAAAATTCCAAATTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAA
          1 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCAA

                           *                                      *         *
        568 AACTTCCAAAAATT-TAGTTTTT-CGACCCCGAAACTTCCAAAAAT-TCCATTTCT-ACCCTC-G
          1 AACTTCCAAAAATTCCA-TTTTTAC--CCCCG-AACTTCCAAAAATCT-CATTTTTGACCC-CAA

                             *          *                               
        628 AACTTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATGC-CATTTTTGACCCCAA
          1 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAAT-CTCATTTTTGACCCCAA

                  *                    *     *                  *    * * 
        687 AACTT-TACAAAATTCCATTTTTACCCTCGAACCTCC-AAAATCTCCATTTTCGACCTCGA
          1 AACTTCCA-AAAATTCCATTTTTACCCCCGAACTTCCAAAAATCT-CATTTTTGACCCCAA

                  **                    
        746 AAC-TCTTAAAATTACCA-TTTTACCCC
          1 AACTTCCAAAAATT-CCATTTTTACCCC

        772 TGGGTATCCG


Statistics
Matches: 216,  Mismatches: 30, Indels: 36
        0.77            0.11        0.13

Matches are distributed among these distances:
  57    1  0.00
  58   43  0.20
  59  120  0.56
  60   30  0.14
  61   22  0.10

ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30


Consensus pattern (59 bp):   
AACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCAA

Found at i:700 original size:119 final size:120

Alignment explanation


    Indices: 472--698  Score: 316
    Period size: 119  Copynumber: 1.9  Consensus size: 120

        462 TTCCATTTTT

                                       *              *                    * 
        472 ACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAACTTTCAAAAATTCCAAATTTACCCTC
          1 ACCCCCAAACTTCCAAAAATCTCATTTCTGACCCCAAAACTTCCAAAAATTCCAAATTTACCCCC

            *                                   *                  
        537 GAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTTAGTTTTTCG
         66 AAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTACAAAAATTTAGTTTTTCG

                 *                                *                  *       
        592 ACCCCGAAACTTCCAAAAAT-TCCATTTCT-ACCCTC-GAACTTCCAAAAATTCCAATTTTACCC
          1 ACCCCCAAACTTCCAAAAATCT-CATTTCTGACCC-CAAAACTTCCAAAAATTCCAAATTTACCC

                            *        *                   
        654 CCAAACTTCCAAAAATGCCATTTTTGACCCCAAAACTTTACAAAA
         64 CCAAACTTCCAAAAATCCCATTTTTAACCCCAAAAC-TTACAAAA

        699 TTCCATTTTT


Statistics
Matches: 94,  Mismatches: 10, Indels: 6
        0.85            0.09        0.05

Matches are distributed among these distances:
 119   61  0.65
 120   33  0.35

ACGTcount: A:0.37, C:0.31, G:0.04, T:0.28


Consensus pattern (120 bp):   
ACCCCCAAACTTCCAAAAATCTCATTTCTGACCCCAAAACTTCCAAAAATTCCAAATTTACCCCC
AAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTACAAAAATTTAGTTTTTCG
Done.