Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001504.1 Kokia drynarioides strain JFW-HI SEQ_113047, 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, 859

Length: 1432
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37


Found at i:935 original size:88 final size:87

Alignment explanation


    Indices: 816--1083  Score: 269
    Period size: 88  Copynumber: 3.0  Consensus size: 87

        806 AGAAATCATG

                     *       *              *          *                   * 
        816 TTTTGACCCCAAACTTCCCAAAATCACATTTTGACCCCAAAACTTCT-TCAAAATTACATTTTGA
          1 TTTTGACCCTAAACTTCTCAAAA-CACATTTTAACCCCAAAACATCTCT-AAAATTACATTTTAA

                   * *               
        880 CTCCT-ACATTTCTCTAAAATTACA
         64 C-CCTAAAACTTCTCTAAAATTACA

                                                               *             
        904 TTTTGACCCTAAACTTCTCAAAACAACATTTTAACCCCAAAACATCTCTAATATTACATTTTAAC
          1 TTTTGACCCTAAACTTCTCAAAAC-ACATTTTAACCCCAAAACATCTCTAAAATTACATTTTAAC

                                   
        969 CCTAAAACTTCTCTAAAATTACA
         65 CCTAAAACTTCTCTAAAATTACA

                          *           *              **     *                
        992 TTTTGACCCTTAAAATTCTCCAAAATTACATTTTTAA--CCTTAAC-TTTCCTAAAATTACATTT
          1 TTTTGACCC-TAAACTTCT-CAAAA-CACA-TTTTAACCCCAAAACATCT-CTAAAATTACATTT

                *         *  *         
       1054 TAACGCT-AAACTTTTCCAAAATTACA
         61 TAACCCTAAAACTTCTCTAAAATTACA

                
       1080 TTTT
          1 TTTT

       1084 AACCTTGAAT


Statistics
Matches: 155,  Mismatches: 17, Indels: 16
        0.82            0.09        0.09

Matches are distributed among these distances:
  87    4  0.03
  88  104  0.67
  89   33  0.21
  90    8  0.05
  91    6  0.04

ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37


Consensus pattern (87 bp):   
TTTTGACCCTAAACTTCTCAAAACACATTTTAACCCCAAAACATCTCTAAAATTACATTTTAACC
CTAAAACTTCTCTAAAATTACA

Found at i:1033 original size:30 final size:29

Alignment explanation


    Indices: 816--1087  Score: 219
    Period size: 30  Copynumber: 9.3  Consensus size: 29

        806 AGAAATCATG

                *    *   *           *   
        816 TTTTGACCCCAAACTTC-CCAAAATCACA
          1 TTTTAACCCTAAAATTCTCCAAAATTACA

                *    *         *          
        844 TTTTGACCCCAAAACTTCTTCAAAATTACA
          1 TTTTAACCCTAAAA-TTCTCCAAAATTACA

                *       * *     *         
        874 TTTTGACTCCTACATTTCTCTAAAATTACA
          1 TTTTAAC-CCTAAAATTCTCCAAAATTACA

                *        *          **   
        904 TTTTGACCCTAAACTTCT-CAAAACAACA
          1 TTTTAACCCTAAAATTCTCCAAAATTACA

                     *     *    *  *      
        932 TTTTAACCCCAAAACATCTCTAATATTACA
          1 TTTTAACCCTAAAA-TTCTCCAAAATTACA

                                *         
        962 TTTTAACCCTAAAACTTCTCTAAAATTACA
          1 TTTTAACCCTAAAA-TTCTCCAAAATTACA

                *                         
        992 TTTTGACCCTTAAAATTCTCCAAAATTACA
          1 TTTTAACCC-TAAAATTCTCCAAAATTACA

                       *  *                
       1022 TTTTTAA-CCTTAACTT-TCCTAAAATTACA
          1 -TTTTAACCCTAAAATTCTCC-AAAATTACA

                   *     *  *            
       1051 TTTTAACGCTAAACTTTTCCAAAATTACA
          1 TTTTAACCCTAAAATTCTCCAAAATTACA

                    
       1080 TTTTAACC
          1 TTTTAACC

       1088 TTGAATTCCC


Statistics
Matches: 202,  Mismatches: 32, Indels: 19
        0.80            0.13        0.08

Matches are distributed among these distances:
  28   40  0.20
  29   52  0.26
  30   96  0.48
  31   14  0.07

ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36


Consensus pattern (29 bp):   
TTTTAACCCTAAAATTCTCCAAAATTACA

Found at i:1078 original size:118 final size:118

Alignment explanation


    Indices: 816--1087  Score: 295
    Period size: 118  Copynumber: 2.3  Consensus size: 118

        806 AGAAATCATG

                *          *          *       *                              
        816 TTTTGACCCC-AAACTTC-CCAAAATCACATTTTGACCCCAAAACTTCTTCAAAATTACATTTTG
          1 TTTTAACCCCAAAACATCTCCAAAATTACATTTTAACCCCAAAACTTCTTCAAAATTACATTTTG

                   * *     *               *                     
        879 ACTCCTACATTTCTCTAAAATTACATTTTGACCCTAAACTTCTCAAAACAACA
         66 ACTCCTAAAATTCTCCAAAATTACATTTTGAACCTAAACTTCTCAAAACAACA

                                *  *               *                         
        932 TTTTAACCCCAAAACATCTCTAATATTACATTTTAACCCTAAAACTTC-TCTAAAATTACATTTT
          1 TTTTAACCCCAAAACATCTCCAAAATTACATTTTAACCCCAAAACTTCTTC-AAAATTACATTTT

                                           *     *              **   
        996 GAC-CCTTAAAATTCTCCAAAATTACATTTTTAACCTTAACTT-TCCTAAAATTACA
         65 GACTCC-TAAAATTCTCCAAAATTACATTTTGAACCTAAACTTCT-C-AAAACAACA

                    * *    * *                    
       1051 TTTTAA-CGCTAAACTTTTCCAAAATTACATTTTAACC
          1 TTTTAACCCCAAAACATCTCCAAAATTACATTTTAACC

       1088 TTGAATTCCC


Statistics
Matches: 129,  Mismatches: 21, Indels: 10
        0.81            0.13        0.06

Matches are distributed among these distances:
 116    9  0.07
 117   11  0.09
 118   96  0.74
 119   13  0.10

ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36


Consensus pattern (118 bp):   
TTTTAACCCCAAAACATCTCCAAAATTACATTTTAACCCCAAAACTTCTTCAAAATTACATTTTG
ACTCCTAAAATTCTCCAAAATTACATTTTGAACCTAAACTTCTCAAAACAACA
Done.