Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010781.1 Kokia drynarioides strain JFW-HI SEQ_125746, 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, 616

Length: 1028
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26


Found at i:657 original size:216 final size:215

Alignment explanation


    Indices: 1--1028  Score: 1262
    Period size: 216  Copynumber: 4.8  Consensus size: 215

                                             *                               
          1 AGTTCATCCAAGAACCAAAAGAGAAACAATTCTGACATAAATAAGTTTTAAATTCAAAGACCAAA
          1 AGTTCATCCAAGAACCAAAAGAGAAACAATTCTCACATAAATAAGTTTTAAATTCAAAGACCAAA

                               *                             *         *     
         66 AGTTGTTTACAAAATGACAGA-ATTTGGACCAAATGATGCGATTTCCCGGGCATGGAATATTCGA
         66 AGTTGTTTACAAAATGACAAACATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGA

                          *           *                         *    *    * *
        130 AAAATTACTCGAAGAAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAATAACTTGA
        131 AAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACTCGT

                            * * 
        195 AAAAGTTTGACAAGTTTGGA
        196 AAAAGTTTGACAAGTTCGTA

                                     *        *  *                           
        215 AGTTCGA-CCAAGAACCAAAAGAGATACAATTCTGACGTAAATAAGTTTTAAATT-------C--
          1 AGTTC-ATCCAAGAACCAAAAGAGAAACAATTCTCACATAAATAAGTTTTAAATTCAAAGACCAA

                  *                  *                               *     * 
        270 ---TTGGTTACAAAAATGACAAACCGTTTGGACCAAATGATGCGATTTCCCGAGCATCGAATGCT
         65 AAGTTGTTTAC-AAAATGACAAA-CATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTT

                     * * *                                 *                 
        332 CGAAAAATTGCACAAAGGAATGGATCGT-TCTGAATACTTTAAGGAATCAAAGTTAAAAAAGAAC
        128 CGAAAAATTACTCGAAGGAATGGATCGTCT-TGAATACTTTAAGGAACCAAAGTTAAAAAAGAAC

              *  ** *       * *     
        396 TCATATTATTTTGACAGGCTCGTA
        192 TCGTAAAAGTTTGACAAGTTCGTA

            *                            *      *             **   *         
        420 TGTTCATCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAAGTTTTTTCATTTAAA-ACCAA
          1 AGTTCATCCAAGAACCAAAAGAGAAACAATTCTCACATAAATAAG-TTTTAAATTCAAAGACC-A

               *                                             * *             
        484 AAATTTGTTTAC-AAATGACAAACTATTTGGACCAAATGATGCGATTTCACAAGCATGGAATGTT
         64 AAAGTTGTTTACAAAATGACAAAC-ATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTT

                                  *   *                            *         
        548 CGAAAAATTACTCGAAGGAATGTATCTTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACT
        128 CGAAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACT

                       *        *  
        613 CGTAAAAGTTTCACAAGTTCATA
        193 CGTAAAAGTTTGACAAGTTCGTA

                 *    *   *                  *  *                            
        636 AGTTCGTCCATGAAACAAAAGAGAAACAATTCTTACGTAAATAAGTTTTAAATTCAAAGACCAAA
          1 AGTTCATCCAAGAACCAAAAGAGAAACAATTCTCACATAAATAAGTTTTAAATTCAAAGACCAAA

                                 *                                           
        701 AGTTGTTTACAAAATGACAGAGCATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCG
         66 AGTTGTTTACAAAATGACA-AACATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCG

                  **                 * **      *            *                
        766 AAAAATGGCTCGAAGGAATGGATCGCCACGAATACGTTAAGGAACCAATGTTAAAAAAGAACTCG
        130 AAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACTCG

                             * * 
        831 TAAAAGTTTGACAAGTTTGGA
        195 TAAAAGTTTGACAAGTTCGTA

                       *    *                *                               
        852 AGTTCATCCAACAACCGAAAGAGAAACAATTCTGACATAAATAAGTTTTAAATTCAAAGACCAAA
          1 AGTTCATCCAAGAACCAAAAGAGAAACAATTCTCACATAAATAAGTTTTAAATTCAAAGACCAAA

                      *                                                     *
        917 AGTTGTTTACGAAATGACAAAGCATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCA
         66 AGTTGTTTACAAAATGACAAA-CATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCG

                                *           *      *       
        982 AAAAATTACTCGAAGGAATGAATCGTCTTGAACACTTTAGGGAACCA
        130 AAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCA


Statistics
Matches: 687,  Mismatches: 102, Indels: 48
        0.82            0.12        0.06

Matches are distributed among these distances:
 202    7  0.01
 203   10  0.01
 204    1  0.00
 205  142  0.21
 206    7  0.01
 207    1  0.00
 212    1  0.00
 214   50  0.07
 215   25  0.04
 216  433  0.63
 217    3  0.00
 218    7  0.01

ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26


Consensus pattern (215 bp):   
AGTTCATCCAAGAACCAAAAGAGAAACAATTCTCACATAAATAAGTTTTAAATTCAAAGACCAAA
AGTTGTTTACAAAATGACAAACATTTGGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGA
AAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACTCGT
AAAAGTTTGACAAGTTCGTA

Done.