Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000072.1 Kokia drynarioides strain JFW-HI SEQ_110647, 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, 705

Length: 1175
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39


Found at i:474 original size:30 final size:29

Alignment explanation


    Indices: 429--840  Score: 287
    Period size: 29  Copynumber: 14.0  Consensus size: 29

        419 AGAGGTCCCT

                                           
        429 AAACTATCCAAAAATTCCATTTTTGACCCCC
          1 AAACT-TCCAAAAATTCCATTTTT-ACCCCC

                     *     *          ** 
        460 AAACTTCCATAAATTTCATTTTTACCATC
          1 AAACTTCCAAAAATTCCATTTTTACCCCC

            *              **         ***
        489 GAACTTCCAAAAATTGGATTTTTACCATT
          1 AAACTTCCAAAAATTCCATTTTTACCCCC

            *                          * 
        518 GAACTTCCAAAAATTCCATTTTTACCCAC
          1 AAACTTCCAAAAATTCCATTTTTACCCCC

            *                            
        547 GAACTTCCAAAAATTCCATTTTTACCCCC
          1 AAACTTCCAAAAATTCCATTTTTACCCCC

            *      *       *           * *
        576 GAACTTCTAAAAATTACATTTTTAACCTCG
          1 AAACTTCCAAAAATTCCATTTTT-ACCCCC

                                      * **
        606 AAACTTCCAAAAATTCCATTTTTGACTCTG
          1 AAACTTCCAAAAATTCCATTTTT-ACCCCC

                                        **
        636 AAACTTCCAAAAAATT-CATTTTTACCCTT
          1 AAACTTCC-AAAAATTCCATTTTTACCCCC

            *           *          *     *
        665 GAACTTCCAAAATTTCCATCTTTGACCCCA
          1 AAACTTCCAAAAATTCCAT-TTTTACCCCC

                         * *             
        695 AAACTTCCAAAAAATACATTTTTACCCCC
          1 AAACTTCCAAAAATTCCATTTTTACCCCC

            *   *  *     *         *   ***
        724 GAACCTCTAAAAAATCCATTTTCAACCTTG
          1 AAACTTCCAAAAATTCCATTTT-TACCCCC

                            *              
        754 AAAC-TCTC-AAAATTAC-TCTTTTACCCCC
          1 AAACTTC-CAAAAATTCCAT-TTTTACCCCC

            *       *    *           *    
        782 GAA-TGTCTAAAATTTCCATTTTTAACCCC
          1 AAACT-TCCAAAAATTCCATTTTTACCCCC

                     *                     
        811 AAACTTTCCCAAAATTACCA-TTTTACCCCC
          1 AAAC-TTCCAAAAATT-CCATTTTTACCCCC

        841 GGGTATCCAA


Statistics
Matches: 302,  Mismatches: 65, Indels: 29
        0.76            0.16        0.07

Matches are distributed among these distances:
  28   12  0.04
  29  171  0.57
  30  103  0.34
  31   16  0.05

ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33


Consensus pattern (29 bp):   
AAACTTCCAAAAATTCCATTTTTACCCCC

Found at i:758 original size:59 final size:59

Alignment explanation


    Indices: 430--841  Score: 358
    Period size: 59  Copynumber: 7.0  Consensus size: 59

        420 GAGGTCCCTA

                                   *     *         *     *          **  
        430 AACTATCCAAAAATTCCATTTTTGACCCCCAAACTTCCATAAATTTCATTTTTACCATCG
          1 AACT-TCCAAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTACATTTTTACCCCCG

                          **           **                *           *  
        490 AACTTCCAAAAATTGGATTTTT-ACCATTG-AACTTCCAAAAATTCCATTTTTACCCACG
          1 AACTTCCAAAAATTCCATTTTTAACC-CCGAAACTTCCAAAAATTACATTTTTACCCCCG

                                   *            *                *  *  
        548 AACTTCCAAAAATTCCATTTTTACCCCCG-AACTTCTAAAAATTACATTTTTAACCTCG
          1 AACTTCCAAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTACATTTTTACCCCCG

                                   *  * *                             ** 
        606 AAACTTCCAAAAATTCCATTTTTGACTCTGAAACTTCCAAAAAATT-CATTTTTACCCTTG
          1 -AACTTCCAAAAATTCCATTTTTAACCCCGAAACTTCC-AAAAATTACATTTTTACCCCCG

                       *      *   *     *             *                
        666 AACTTCCAAAATTTCCATCTTTGACCCCAAAACTTCCAAAAAATACATTTTTACCCCCG
          1 AACTTCCAAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTACATTTTTACCCCCG

               *  *     *        *    **                                 
        725 AACCTCTAAAAAATCCATTTTCAACCTTGAAAC-TCTC-AAAATTAC-TCTTTTACCCCCG
          1 AACTTCCAAAAATTCCATTTTTAACCCCGAAACTTC-CAAAAATTACAT-TTTTACCCCCG

                   *    *                          *                      
        783 AA-TGTCTAAAATTTCCATTTTTAACCCC-AAACTTTCCCAAAATTACCA-TTTTACCCCCG
          1 AACT-TCCAAAAATTCCATTTTTAACCCCGAAAC-TTCCAAAAATTA-CATTTTTACCCCCG

        842 GGTATCCAAA


Statistics
Matches: 288,  Mismatches: 50, Indels: 29
        0.78            0.14        0.08

Matches are distributed among these distances:
  57    5  0.02
  58  122  0.42
  59  131  0.45
  60   23  0.08
  61    7  0.02

ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33


Consensus pattern (59 bp):   
AACTTCCAAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTACATTTTTACCCCCG
Done.