Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006076.1 Kokia drynarioides strain JFW-HI SEQ_120559, 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, 600

Length: 1000
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28


Found at i:400 original size:215 final size:216

Alignment explanation


    Indices: 8--984  Score: 1080
    Period size: 215  Copynumber: 4.5  Consensus size: 216

          1 TTCGACT

                *              *          * *       *            *           
          8 AGTTTGGAAGTTCATCCAAAAACCAAGAGACACACAATTCACACGTAAATAAGCTTTTAATTCAA
          1 AGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA

               *             *       *   *               *     *      *      
         73 AGATCAAAACTTGTTTATAAAATGAGAAATTATTTAGACCAAATGGTGCGATTTCCCTCA-CATG
         66 AGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTCCC-GAGCATG

               **    *          *           ** *  *                          
        137 GAACATTCGGAAAATTACTCAAAGGAATGGATTGTGTTAAACACTTTAAGGAACCGGATTTAAAA
        130 GAATGTTCGAAAAATTACTCGAAGGAATGGATCATCTTGAACACTTTAAGGAACCGGATTTAAAA

                                  
        202 AAGAACTCGTAAAAGTTTGACA
        195 AAGAACTCGTAAAAGTTTGACA

             *  **                    *                                    * 
        224 ATTTTAGAAGTTCATCCAACAACCAATAGAGAAACAATTCTCACGTAAATAAG-TTTTAATTCGA
          1 AGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA

              *                      *     *      *        *        *       *
        288 AGGCCAAAACTTGTTTACAAAATGACAAACTCTTTAGAGCAAATGATTCGACTTCCAGAGCATGT
         66 AGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGG

                  *        *         *              *        *     * *   *   
        353 AATGTTTGAAAAATTGCTCGAAGGATTGGATCATCTTGAATACTTTAAGAAACCGAAGTTATAAA
        131 AATGTTCGAAAAATTACTCGAAGGAATGGATCATCTTGAACACTTTAAGGAACCGGATTTAAAAA

                                 
        418 AGAACTCGTAAAAGTTTGACA
        196 AGAACTCGTAAAAGTTTGACA

                *        *     *            *          *                     
        439 AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGACACAATTCTCATGTAAATAAGTTTTTAATTCAA
          1 AGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA

               **       *                                      *     **      
        504 AGATTAAAACTTATTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGG
         66 AGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGG

                *   ***         * *         *     *              *           
        569 AATGGTCGGGGAATTACTC-TACGAATGGATCGTCTTGGACACTTTAAGGAACTGGATTTAAAAA
        131 AATGTTCGAAAAATTACTCGAAGGAATGGATCATCTTGAACACTTTAAGGAACCGGATTTAAAAA

             *    *          *   
        633 ATAACTTGTAAAAGTTTAACA
        196 AGAACTCGTAAAAGTTTGACA

                         * *                     *        *                  
        654 AGTTCGGAAGTTCGTTCAACAACCAAGAGAGAAACAACTCTCACGTTAATAAGTTTTTAATTCAA
          1 AGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA

              *      *        *      *     *               *                *
        719 AGGCCAAAATTTGTTTACTAAATGACAAACTCTTTAGACCAAATGATTCGACTTCCCGAGCATGT
         66 AGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGG

                  *        *         *              *                  *  *  
        784 AATGTTTGAAAAATTGCTCGAAGGATTGGATCATCTTGAATACTTTAAGGAACC-GATGCTATAA
        131 AATGTTCGAAAAATTACTCGAAGGAATGGATCATCTTGAACACTTTAAGGAACCGGAT-TTAAAA

                  *               
        848 AAGAACACGTAAAAGTTTGACA
        195 AAGAACTCGTAAAAGTTTGACA

                     *      *  *                    *             *          
        870 AGTTCGGAACTTCATCAAATAACCAAGAGAGAAACAATTCGCACGTAAATAAGTCTTTAATTCAA
          1 AGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA

                 *             *    *                         
        935 AGATCAATAAACTTGTTTAAAAAACGAAAAACTATTTAGACCAAATGATG
         66 AGA-CCA-AAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATG

        985 AAATTTCCCA


Statistics
Matches: 620,  Mismatches: 135, Indels: 10
        0.81            0.18        0.01

Matches are distributed among these distances:
 214    1  0.00
 215  354  0.57
 216  228  0.37
 217    2  0.00
 218   35  0.06

ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28


Consensus pattern (216 bp):   
AGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
AGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGG
AATGTTCGAAAAATTACTCGAAGGAATGGATCATCTTGAACACTTTAAGGAACCGGATTTAAAAA
AGAACTCGTAAAAGTTTGACA

Found at i:811 original size:431 final size:431

Alignment explanation


    Indices: 8--993  Score: 1427
    Period size: 431  Copynumber: 2.3  Consensus size: 431

          1 TTCGACT

                                          *                      *           
          8 AGTTTGGAAGTTCATCCAAAAACCAAGAGACACACAATTCACACGTAAATAAGCTTTTAATTCAA
          1 AGTTTGGAAGTTCATCCAAAAACCAAGAGAGACACAATTCACACGTAAATAAGTTTTTAATTCAA

                *            *       *   *               *                   
         73 AGATCAAAACTTGTTTATAAAATGAGAAATTATTTAGACCAAATGGTGCGATTTCCCTCACATGG
         66 AGATAAAAACTTGTTTAAAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCACATGG

                *                 *        *  *                              
        138 AACATTCGGAAAATTACTCAAAGGAATGGATTGTGTTAAACACTTTAAGGAACCGGATTTAAAAA
        131 AACAGTCGGAAAATTACTCAAACGAATGGATCGTCTTAAACACTTTAAGGAACCGGATTTAAAAA

                             *    *  *                     *          *      
        203 AGAACTCGTAAAAGTTTGACAATTTTAGAAGTTCATCCAACAACCAATAGAGAAACAATTCTCAC
        196 AGAACTCGTAAAAGTTTAACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAACTCTCAC

                              *                                       *      
        268 GTAAATAAGTTTTAATTCGAAGGCCAAAACTTGTTTACAAAATGACAAACTCTTTAGAGCAAATG
        261 GTAAATAAGTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTCTTTAGACCAAATG

                                                                             
        333 ATTCGACTTCCAGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCATCTTGAATACTT
        326 ATTCGACTTCCAGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCATCTTGAATACTT

                         *           *               
        398 TAAGAAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACA
        391 TAAGAAACCGAAGCTATAAAAGAACACGTAAAAGTTTGACA

                         *     *                    *  *                     
        439 AGTTTGGAAGTTCGTCCAAGAACCAAGAGAGACACAATTCTCATGTAAATAAGTTTTTAATTCAA
          1 AGTTTGGAAGTTCATCCAAAAACCAAGAGAGACACAATTCACACGTAAATAAGTTTTTAATTCAA

                *       *    *                                         *     
        504 AGATTAAAACTTATTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGG
         66 AGATAAAAACTTGTTTAAAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCACATGG

              **     **         *                **              *           
        569 AATGGTCGGGGAATTACTC-TACGAATGGATCGTCTTGGACACTTTAAGGAACTGGATTTAAAAA
        131 AACAGTCGGAAAATTACTCAAACGAATGGATCGTCTTAAACACTTTAAGGAACCGGATTTAAAAA

             *    *                   *       * *                            
        633 ATAACTTGTAAAAGTTTAACAAGTTCGGAAGTTCGTTCAACAACCAAGAGAGAAACAACTCTCAC
        196 AGAACTCGTAAAAGTTTAACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAACTCTCAC

              *                           *        *                         
        698 GTTAATAAGTTTTTAATTCAAAGGCCAAAATTTGTTTACTAAATGACAAACTCTTTAGACCAAAT
        261 GTAAATAAG-TTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTCTTTAGACCAAAT

                        *                                                    
        763 GATTCGACTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCATCTTGAATACT
        325 GATTCGACTTCCAGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCATCTTGAATACT

                 *      *                             
        828 TTAAGGAACCGATGCTATAAAAGAACACGTAAAAGTTTGACA
        390 TTAAGAAACCGAAGCTATAAAAGAACACGTAAAAGTTTGACA

                *    *                       *       *             *         
        870 AGTTCGGAACTTCAT-CAAATAACCAAGAGAGAAACAATTCGCACGTAAATAAGTCTTTAATTCA
          1 AGTTTGGAAGTTCATCCAAA-AACCAAGAGAGACACAATTCACACGTAAATAAGTTTTTAATTCA

                                     *                         **       
        934 AAGATCAATAAACTTGTTTAAAAAACGAAAAACTATTTAGACCAAATGATGAAATTTCCC
         65 AAGAT-AA-AAACTTGTTTAAAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCC

        994 AAACATG


Statistics
Matches: 492,  Mismatches: 59, Indels: 6
        0.88            0.11        0.01

Matches are distributed among these distances:
 430  104  0.21
 431  341  0.69
 432    1  0.00
 433   46  0.09

ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28


Consensus pattern (431 bp):   
AGTTTGGAAGTTCATCCAAAAACCAAGAGAGACACAATTCACACGTAAATAAGTTTTTAATTCAA
AGATAAAAACTTGTTTAAAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCACATGG
AACAGTCGGAAAATTACTCAAACGAATGGATCGTCTTAAACACTTTAAGGAACCGGATTTAAAAA
AGAACTCGTAAAAGTTTAACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAACTCTCAC
GTAAATAAGTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTCTTTAGACCAAATG
ATTCGACTTCCAGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCATCTTGAATACTT
TAAGAAACCGAAGCTATAAAAGAACACGTAAAAGTTTGACA

Done.