Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006010.1 Kokia drynarioides strain JFW-HI SEQ_120448, 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: 8824
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33


Found at i:8417 original size:18 final size:18

Alignment explanation


    Indices: 8391--8515  Score: 133
    Period size: 18  Copynumber: 6.9  Consensus size: 18

       8381 ATGTAGCTTG

                      *       
       8391 TTTGAGCATATTGGCTCA
          1 TTTGAGCATACTGGCTCA

              *              *
       8409 TTAGAGCATACTGGCTCG
          1 TTTGAGCATACTGGCTCA

                        *     
       8427 TTTGAGCATACTAGCTCA
          1 TTTGAGCATACTGGCTCA

              *               
       8445 TTAGAGCATACTGGCTCA
          1 TTTGAGCATACTGGCTCA

                   *  *      *
       8463 TTTGAGCGTAGTGGCTCG
          1 TTTGAGCATACTGGCTCA

                        *   **
       8481 TTTGAGCATACTAGCTTG
          1 TTTGAGCATACTGGCTCA

               *        *    
       8499 TTTAAGCATACTAGCTC
          1 TTTGAGCATACTGGCTC

       8516 GTAAGAGCAT


Statistics
Matches: 89,  Mismatches: 18, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  18   89  1.00

ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34


Consensus pattern (18 bp):   
TTTGAGCATACTGGCTCA

Found at i:8444 original size:36 final size:36

Alignment explanation


    Indices: 8355--8531  Score: 176
    Period size: 36  Copynumber: 4.9  Consensus size: 36

       8345 AGAAACGAAA

                    *                *   * *   *
       8355 GTTTGAGCCTACTGGCTCGTTAGAGAAT-GTAGCTT
          1 GTTTGAGCATACTGGCTCGTTAGAGCATACTGGCTC

                       *      *                 
       8390 GTTTGAGCATATTGGCTCATTAGAGCATACTGGCTC
          1 GTTTGAGCATACTGGCTCGTTAGAGCATACTGGCTC

                         *    *                 
       8426 GTTTGAGCATACTAGCTCATTAGAGCATACTGGCTC
          1 GTTTGAGCATACTGGCTCGTTAGAGCATACTGGCTC

            *       *  *         *         *   *
       8462 ATTTGAGCGTAGTGGCTCGTTTGAGCATACTAGCTT
          1 GTTTGAGCATACTGGCTCGTTAGAGCATACTGGCTC

                *        *      *             
       8498 GTTTAAGCATACTAGCTCGTAAGAGCATTACTGG
          1 GTTTGAGCATACTGGCTCGTTAGAGCA-TACTGG

       8532 ATCGCAAGAG


Statistics
Matches: 115,  Mismatches: 25, Indels: 2
        0.81            0.18        0.01

Matches are distributed among these distances:
  35   24  0.21
  36   86  0.75
  37    5  0.04

ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33


Consensus pattern (36 bp):   
GTTTGAGCATACTGGCTCGTTAGAGCATACTGGCTC

Found at i:8454 original size:54 final size:54

Alignment explanation


    Indices: 8359--8531  Score: 170
    Period size: 54  Copynumber: 3.2  Consensus size: 54

       8349 ACGAAAGTTT

                *            *   *   *     **  *       *          
       8359 GAGCCTACTGGCTCGTTAGAGAAT-GTAGCTTGTTTGAGCATATTGGCTCATTA
          1 GAGCATACTGGCTCGTTTGAGCATACTAGCTCATTAGAGCATACTGGCTCATTA

                                                                 *
       8412 GAGCATACTGGCTCGTTTGAGCATACTAGCTCATTAGAGCATACTGGCTCATTT
          1 GAGCATACTGGCTCGTTTGAGCATACTAGCTCATTAGAGCATACTGGCTCATTA

                *  *                        **            *    * * 
       8466 GAGCGTAGTGGCTCGTTTGAGCATACTAGCTTGTTTA-AGCATACTAGCTCGTAA
          1 GAGCATACTGGCTCGTTTGAGCATACTAGC-TCATTAGAGCATACTGGCTCATTA

                        
       8520 GAGCATTACTGG
          1 GAGCA-TACTGG

       8532 ATCGCAAGAG


Statistics
Matches: 98,  Mismatches: 19, Indels: 4
        0.81            0.16        0.03

Matches are distributed among these distances:
  53   21  0.21
  54   68  0.69
  55    9  0.09

ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32


Consensus pattern (54 bp):   
GAGCATACTGGCTCGTTTGAGCATACTAGCTCATTAGAGCATACTGGCTCATTA

Found at i:8524 original size:18 final size:18

Alignment explanation


    Indices: 8359--8525  Score: 122
    Period size: 18  Copynumber: 9.3  Consensus size: 18

       8349 ACGAAAGTTT

                *    *        
       8359 GAGCCTACTGGCTCGTTA
          1 GAGCATACTAGCTCGTTA

               *   *     *   *
       8377 GAGAAT-GTAGCTTGTTT
          1 GAGCATACTAGCTCGTTA

                   * *    *   
       8394 GAGCATATTGGCTCATTA
          1 GAGCATACTAGCTCGTTA

                     *       *
       8412 GAGCATACTGGCTCGTTT
          1 GAGCATACTAGCTCGTTA

                          *   
       8430 GAGCATACTAGCTCATTA
          1 GAGCATACTAGCTCGTTA

                     *    *  *
       8448 GAGCATACTGGCTCATTT
          1 GAGCATACTAGCTCGTTA

                *  * *       *
       8466 GAGCGTAGTGGCTCGTTT
          1 GAGCATACTAGCTCGTTA

                         *     
       8484 GAGCATACTAGCTTGTTTA
          1 GAGCATACTAGCTCG-TTA

                            * 
       8503 -AGCATACTAGCTCGTAA
          1 GAGCATACTAGCTCGTTA

                  
       8520 GAGCAT
          1 GAGCAT

       8526 TACTGGATCG


Statistics
Matches: 116,  Mismatches: 30, Indels: 6
        0.76            0.20        0.04

Matches are distributed among these distances:
  17   14  0.12
  18  100  0.86
  19    2  0.02

ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32


Consensus pattern (18 bp):   
GAGCATACTAGCTCGTTA
Done.