Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007294.1 Kokia drynarioides strain JFW-HI SEQ_121910, 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: 6802
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31


Found at i:633 original size:30 final size:29

Alignment explanation


    Indices: 599--711  Score: 104
    Period size: 30  Copynumber: 3.8  Consensus size: 29

        589 TAAACTATCC

                               *          
        599 AAAAATTCCATTTTTGACCTCGAAACTTTA
          1 AAAAATTCCATTTTT-ACCCCGAAACTTTA

                   **           *       * 
        629 AAAAATTATATTTTTACCCCCAAACTTCCA
          1 AAAAATTCCATTTTTACCCCGAAACTT-TA

                                 *       *
        659 AAAAA-TCCATTTTTAACCCCAAAACTTTG
          1 AAAAATTCCATTTTT-ACCCCGAAACTTTA

                                     
        688 AAAAATTACCATTTTT-CCCTCGAA
          1 AAAAATT-CCATTTTTACCC-CGAA

        712 TGTTCGAAAA


Statistics
Matches: 67,  Mismatches: 11, Indels: 10
        0.76            0.12        0.11

Matches are distributed among these distances:
  29   25  0.37
  30   34  0.51
  31    8  0.12

ACGTcount: A:0.39, C:0.24, G:0.04, T:0.34


Consensus pattern (29 bp):   
AAAAATTCCATTTTTACCCCGAAACTTTA

Found at i:731 original size:59 final size:58

Alignment explanation


    Indices: 598--879  Score: 185
    Period size: 59  Copynumber: 4.8  Consensus size: 58

        588 CTAAACTATC

                      *     *     *        *         *          * *     *
        598 CAAAAATTCCATTTTTGACCTCGAAACTTT-AAAAAATTA-TATTTTTACCCCCAAACTTC
          1 CAAAAATTCCTTTTTTAACC-CCAAACTTTCTAAAAATTACCA-TTTTACCCTCGAA-TTT

                  *   *                    *               *            
        657 CAAAAAATCCATTTTTAACCCCAAAACTTT-GAAAAATTACCATTTTTCCCTCGAATGTT
          1 CAAAAATTCCTTTTTTAACCCC-AAACTTTCTAAAAATTACCATTTTACCCTCGAAT-TT

             *              * *     **             *                  *
        716 CGAAAATTCCTTTTTTGATCCCAATTTTTCTAAAAATTAACATTTTACCCTCGAATATC
          1 CAAAAATTCCTTTTTTAACCCCAAACTTTCTAAAAATTACCATTTTACCCTCGAAT-TT

                               *   * ***                  *     *     * 
        775 CAAAAATT-CTATTTTTGATCCCGATTTTTTCTAAAAATTACCATTGTACCCCCGAATAT
          1 CAAAAATTCCT-TTTTT-AACCCCAAACTTTCTAAAAATTACCATTTTACCCTCGAATTT

             *        *                   **              
        834 CTAAAATTCCCTTTTTAACCCCAAACTTTCCCAAAATTACCATTTT
          1 CAAAAATTCCTTTTTTAACCCCAAACTTTCTAAAAATTACCATTTT

        880 GCCCCTAAAG


Statistics
Matches: 174,  Mismatches: 42, Indels: 15
        0.75            0.18        0.06

Matches are distributed among these distances:
  58   31  0.18
  59  109  0.63
  60   34  0.20

ACGTcount: A:0.34, C:0.24, G:0.04, T:0.37


Consensus pattern (58 bp):   
CAAAAATTCCTTTTTTAACCCCAAACTTTCTAAAAATTACCATTTTACCCTCGAATTT

Found at i:825 original size:60 final size:59

Alignment explanation


    Indices: 688--879  Score: 208
    Period size: 59  Copynumber: 3.3  Consensus size: 59

        678 CAAAACTTTG

                           *         * * *                             
        688 AAAAATTACCATTTTTCCCTCGAATGTTCGAAAATTCCTTTTTTGATCCCAATTTTTCT
          1 AAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCTTTTTTGATCCCAATTTTTCT

                    *                                            *       
        747 AAAAATTAACATTTTACCCTCGAATATCCAAAAATT-CTATTTTTGATCCCGATTTTTTCT
          1 AAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCT-TTTTTGATCCC-AATTTTTCT

                         *     *         *        *     * *     **    *
        807 AAAAATTACCATTGTACCCCCGAATAT-CTAAAATTCCCTTTTTAACCCCAAACTTTCC
          1 AAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCTTTTTTGATCCCAATTTTTCT

            *              
        865 CAAAATTACCATTTT
          1 AAAAATTACCATTTT

        880 GCCCCTAAAG


Statistics
Matches: 111,  Mismatches: 19, Indels: 7
        0.81            0.14        0.05

Matches are distributed among these distances:
  58   20  0.18
  59   58  0.52
  60   33  0.30

ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39


Consensus pattern (59 bp):   
AAAAATTACCATTTTACCCTCGAATATCCAAAAATTCCTTTTTTGATCCCAATTTTTCT

Found at i:6462 original size:6 final size:6

Alignment explanation


    Indices: 6431--6500  Score: 81
    Period size: 6  Copynumber: 11.5  Consensus size: 6

       6421 TTCAATAAAT

                                   *                        *         
       6431 AAAAG- AAAAGAA AAAAGA AGAAGA AAAAGA AAAA-A CAAAAAA AAAGAGA
          1 AAAAGA AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA AAA-AGA

                                    
       6480 AAAAGA AAAAGA AAAAGA AAA
          1 AAAAGA AAAAGA AAAAGA AAA

       6501 GGAGAGGTCG


Statistics
Matches: 57,  Mismatches: 3, Indels: 9
        0.83            0.04        0.13

Matches are distributed among these distances:
   5    6  0.11
   6   40  0.70
   7   11  0.19

ACGTcount: A:0.83, C:0.01, G:0.16, T:0.00


Consensus pattern (6 bp):   
AAAAGA
Done.