Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003014.1 Kokia drynarioides strain JFW-HI SEQ_115526, 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, 891

Length: 1485
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37


Found at i:725 original size:30 final size:30

Alignment explanation


    Indices: 691--853  Score: 126
    Period size: 28  Copynumber: 5.6  Consensus size: 30

        681 ATTTATGACT

                                          
        691 TCGAAACTTCAAAAAATTATATTTTTACAC
          1 TCGAAACTTCAAAAAATTATATTTTTACAC

                       *             *     
        721 TCG-AACTTC-CAAAATTATATTTTCA-ACC
          1 TCGAAACTTCAAAAAATTATATTTTTACA-C

             *                 *      *   
        749 TTGAAACTTCAAAAAATTACATTTTTCCAC
          1 TCGAAACTTCAAAAAATTATATTTTTACAC

                      *                     
        779 T-G-AACTTCCAAAAATT-TCATTTTTGAC-C
          1 TCGAAACTTCAAAAAATTAT-ATTTTT-ACAC

            *        **        *          
        807 CCGAAACTTTTAAAAATTACATTTTTAC-C
          1 TCGAAACTTCAAAAAATTATATTTTTACAC

            * *       *       
        836 CCTAAACTTCCAAAAATT
          1 TCGAAACTTCAAAAAATT

        854 CCATTTTTGA


Statistics
Matches: 107,  Mismatches: 17, Indels: 19
        0.75            0.12        0.13

Matches are distributed among these distances:
  27    1  0.01
  28   37  0.35
  29   33  0.31
  30   35  0.33
  31    1  0.01

ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36


Consensus pattern (30 bp):   
TCGAAACTTCAAAAAATTATATTTTTACAC

Found at i:865 original size:59 final size:59

Alignment explanation


    Indices: 643--880  Score: 248
    Period size: 58  Copynumber: 4.1  Consensus size: 59

        633 TGAACTGTTC

                      *    *    *              *      *    **          
        643 AAAAATTACAATTTTGCCCCCGAACTTCCAAAAATCCCATTTATGACTTCGAAACTTCA
          1 AAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCA

                    *         *                  **     **   **         
        702 AAAAATTATATTTTTA-CACTCGAACTTCC-AAAATTATATTTTCAACCTTGAAACTTCA
          1 AAAAATTACATTTTTACCCCT-GAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCA

                              *                 *                    **
        760 AAAAATTACATTTTT-CCACTGAACTTCCAAAAATTTCATTTTTGACCCCGAAACTTTT
          1 AAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCA

                                 *                            *         
        818 AAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCTAAACTCTCA
          1 AAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACT-TCA

               
        878 AAA
          1 AAA

        881 TTACCCTTTT


Statistics
Matches: 146,  Mismatches: 28, Indels: 9
        0.80            0.15        0.05

Matches are distributed among these distances:
  57    8  0.05
  58   77  0.53
  59   57  0.39
  60    4  0.03

ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34


Consensus pattern (59 bp):   
AAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCA

Found at i:869 original size:30 final size:29

Alignment explanation


    Indices: 642--895  Score: 167
    Period size: 29  Copynumber: 8.7  Consensus size: 29

        632 CTGAACTGTT

                       *    *    **      
        642 CAAAAATTACAATTTTGCCCCCGAACTTC
          1 CAAAAATTACATTTTTACCCCTAAACTTC

                   **       *  ** *       
        671 CAAAAATCCCATTTATGACTTCGAAACTTC
          1 CAAAAATTACATTT-TTACCCCTAAACTTC

            *        *         *   *      
        701 AAAAAATTATATTTTTA-CACTCGAACTTC
          1 CAAAAATTACATTTTTACCCCT-AAACTTC

                     *     * *  *         
        730 C-AAAATTATATTTTCAACCTTGAAACTTC
          1 CAAAAATTACATTTTTACCCCT-AAACTTC

            *                  *  *      
        759 AAAAAATTACATTTTT-CCACTGAACTTC
          1 CAAAAATTACATTTTTACCCCTAAACTTC

                    *             *      *
        787 CAAAAATTTCATTTTTGACCCCGAAACTTT
          1 CAAAAATTACATTTTT-ACCCCTAAACTTC

            *                            
        817 TAAAAATTACATTTTTACCCCTAAACTTC
          1 CAAAAATTACATTTTTACCCCTAAACTTC

                    *                     
        846 CAAAAATTCCATTTTTGACCCCTAAAC-TC
          1 CAAAAATTACATTTTT-ACCCCTAAACTTC

                       **         
        875 TC-AAAATTACCCTTTTACCCC
          1 -CAAAAATTACATTTTTACCCC

        896 CGGATGTCTA


Statistics
Matches: 171,  Mismatches: 46, Indels: 17
        0.73            0.20        0.07

Matches are distributed among these distances:
  28   40  0.23
  29   67  0.39
  30   64  0.37

ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34


Consensus pattern (29 bp):   
CAAAAATTACATTTTTACCCCTAAACTTC

Found at i:880 original size:29 final size:28

Alignment explanation


    Indices: 752--884  Score: 110
    Period size: 30  Copynumber: 4.5  Consensus size: 28

        742 TTCAACCTTG

                                       *  
        752 AAACTTCAAAAAATTACATTTTT--CCACT
          1 AAACTTC--AAAATTACATTTTTGACCCCT

            *              *             *
        780 GAACTTCCAAAAATTTCATTTTTGACCCCG
          1 AAACTT-C-AAAATTACATTTTTGACCCCT

                    *                     
        810 AAACTTTTAAAAATTACATTTTT-ACCCCT
          1 AAAC--TTCAAAATTACATTTTTGACCCCT

                           *              
        839 AAACTTCCAAAAATTCCATTTTTGACCCCT
          1 AAACTT-C-AAAATTACATTTTTGACCCCT

                            
        869 AAACTCTCAAAATTAC
          1 AAACT-TCAAAATTAC

        885 CCTTTTACCC


Statistics
Matches: 85,  Mismatches: 11, Indels: 17
        0.75            0.10        0.15

Matches are distributed among these distances:
  27    2  0.02
  28   19  0.22
  29   30  0.35
  30   31  0.36
  31    1  0.01
  32    2  0.02

ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35


Consensus pattern (28 bp):   
AAACTTCAAAATTACATTTTTGACCCCT

Done.