Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000864.1 Kokia drynarioides strain JFW-HI SEQ_111978, 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: 1707
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34


Found at i:73 original size:21 final size:21

Alignment explanation


    Indices: 49--136  Score: 151
    Period size: 21  Copynumber: 4.2  Consensus size: 21

         39 AAAGAAAACC

                         *        
         49 GTTTGGATCTAG-GCTAGATCT
          1 GTTT-GATCTAGACCTAGATCT

                                 
         70 GTTTGATCTAGACCTAGATCT
          1 GTTTGATCTAGACCTAGATCT

                                 
         91 GTTTGATCTAGACCTAGATCT
          1 GTTTGATCTAGACCTAGATCT

                                 
        112 GTTTGATCTAGACCTAGATCT
          1 GTTTGATCTAGACCTAGATCT

                
        133 GTTT
          1 GTTT

        137 TTTTTTAAAG


Statistics
Matches: 65,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  20    7  0.11
  21   58  0.89

ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40


Consensus pattern (21 bp):   
GTTTGATCTAGACCTAGATCT

Found at i:977 original size:29 final size:29

Alignment explanation


    Indices: 934--1218  Score: 191
    Period size: 29  Copynumber: 9.7  Consensus size: 29

        924 TAAATTGTTC

                                  *       
        934 AAAAATCTC-ATTTTTACCCCCGAACTTCT
          1 AAAAATC-CAATTTTTACCCCCAAACTTCT

                           *   ***      * 
        963 AAAAATCCAAATTTTAACCTAAAAACTTTT
          1 AAAAATCC-AATTTTTACCCCCAAACTTCT

                           *   * *       *
        993 AAAAATCCCAATTTTAACCTCGAAACTTCC
          1 AAAAAT-CCAATTTTTACCCCCAAACTTCT

                                    * *   
       1023 AAAAATTCC-ATTTTTACCCCCAATCCTC-
          1 AAAAA-TCCAATTTTTACCCCCAAACTTCT

            *         *                   
       1051 CAAAATCCCATTTTTTACCCCCAAACTTCT
          1 AAAAAT-CCAATTTTTACCCCCAAACTTCT

                                 *       *
       1081 AAAAATCCAATTTTTAACCCCAAAACTTCC
          1 AAAAATCCAATTTTT-ACCCCCAAACTTCT

                    *     *     *  *   * 
       1111 AAAAATCCCATTTTAACCCCGAAGCTTTT
          1 AAAAATCCAATTTTTACCCCCAAACTTCT

                    *           *    *  *
       1140 AAAAATCCCATTTTTACCCCTAAACCTCC
          1 AAAAATCCAATTTTTACCCCCAAACTTCT

                            *     *   ** *
       1169 AAAAATCTC-ATTTTTGCCCCCGAACCCCC
          1 AAAAATC-CAATTTTTACCCCCAAACTTCT

                      *          
       1198 AAAAATCCCATTTTTTACCCC
          1 AAAAAT-CCAATTTTTACCCC

       1219 AAATTTTTTT


Statistics
Matches: 204,  Mismatches: 41, Indels: 21
        0.77            0.15        0.08

Matches are distributed among these distances:
  27    1  0.00
  28    7  0.03
  29  108  0.53
  30   85  0.42
  31    3  0.01

ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30


Consensus pattern (29 bp):   
AAAAATCCAATTTTTACCCCCAAACTTCT

Found at i:1085 original size:58 final size:58

Alignment explanation


    Indices: 933--1221  Score: 247
    Period size: 58  Copynumber: 4.9  Consensus size: 58

        923 CTAAATTGTT

                    *      *      *      *         *     *   **     * *
        933 CAAAAATCTCATTTTTACCCCCGAACTTCTAAAAATCCAAATTTTAACCTAAAAACTTT
          1 CAAAAATCCCATTTTAACCCCCAAACTTCCAAAAATCC-CATTTTTACCCCAAAACCTC

            *                   * *              *             *  *    
        992 TAAAAATCCCAATTTTAACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCAATCCTC
          1 CAAAAATCCC-ATTTTAACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAAACCTC

                            *             *        *                 *  
       1051 C-AAAATCCCATTTTTTACCCCCAAACTTCTAAAAATCCAATTTTTAACCCCAAAACTTC
          1 CAAAAATCCCA-TTTTAACCCCCAAACTTCCAAAAATCCCATTTTT-ACCCCAAAACCTC

                                 *  *   **                    *       
       1110 CAAAAATCCCATTTTAACCCCGAAGCTTTTAAAAATCCCATTTTTACCCCTAAACCTC
          1 CAAAAATCCCATTTTAACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAAACCTC

                    *      **     *   **                          
       1168 CAAAAATCTCATTTTTGCCCCCGAACCCCCAAAAATCCCATTTTTTACCCCAAA
          1 CAAAAATCCCATTTTAACCCCCAAACTTCCAAAAATCCCA-TTTTTACCCCAAA

       1222 TTTTTTTTTC


Statistics
Matches: 181,  Mismatches: 44, Indels: 10
        0.77            0.19        0.04

Matches are distributed among these distances:
  57    1  0.01
  58   77  0.43
  59   72  0.40
  60   31  0.17

ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30


Consensus pattern (58 bp):   
CAAAAATCCCATTTTAACCCCCAAACTTCCAAAAATCCCATTTTTACCCCAAAACCTC
Done.