Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004213.1 Kokia drynarioides strain JFW-HI SEQ_117461, 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: 10908
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35


Found at i:7260 original size:157 final size:158

Alignment explanation


    Indices: 6969--7431  Score: 540
    Period size: 157  Copynumber: 2.9  Consensus size: 158

       6959 TTTTGGGTGT

                          *           *                                    * 
       6969 TGGTCTTGGATGTCTTACCGATGGCTAAGATCTTGCAATTGTTACAGATTCTCCA-AGCTCGTAT
          1 TGGTCTTGGATGTCCTACCGATGGCTGAGATCTTGCAATTGTTACAGATTCTCCACAGCTCGTGT

               *                     *    *  * *                *            
       7033 GAGCAGCATCGTGTAGCTTAACATCTCGACTCAAAACTCGTGTGAGTAGGCCTATTTCACAGATC
         66 GAGTAGCATCGTGTAGCTTAACATCCCGACCCATAGCTCGTGTGAGTAGGCCCATTTCACAGATC

            *      * *    *           * 
       7098 GTGTGAGTCGTACAGGATAT-AGAGTGC
        131 ATGTGAGCCATACAAGATATAAGAGTAC

                   **                    *          *                        
       7125 TGGTCTTAAATGTCCTACCGATGGCTGAGGTCTTGCAATTATTACAGATTCTCCACAGCTCGTGT
          1 TGGTCTTGGATGTCCTACCGATGGCTGAGATCTTGCAATTGTTACAGATTCTCCACAGCTCGTGT

                 *               *                              *       *    
       7190 GAGTAACATCGTGTAGCTTAAGATCCCGACCCATAGCTCGTGTGAGTAGGCCGATTTCACTGATC
         66 GAGTAGCATCGTGTAGCTTAACATCCCGACCCATAGCTCGTGTGAGTAGGCCCATTTCACAGATC

                                   *    
       7255 ATGTGAGCCATACAAGATATAAGGGTAC
        131 ATGTGAGCCATACAAGATATAAGAGTAC

               **                 * *      *           * *            *      
       7283 T-GAATTGGATGTCCTACCGATAGTTGAGATTTTGCAATTGTTGCTGATTCTCCACAGGTCGTGT
          1 TGGTCTTGGATGTCCTACCGATGGCTGAGATCTTGCAATTGTTACAGATTCTCCACAGCTCGTGT

                                                   *      **               * 
       7347 GA-TCAGCATCGTGTAGCTTAACATCCCGACCCATAGCTTGTGTGAACAGGCCCATTTCACAGCT
         66 GAGT-AGCATCGTGTAGCTTAACATCCCGACCCATAGCTCGTGTGAGTAGGCCCATTTCACAGAT

             *   *                
       7411 CGTGTAAG-CATTACAAGATAT
        130 CATGTGAGCCA-TACAAGATAT

       7432 GGATATTTTA


Statistics
Matches: 259,  Mismatches: 44, Indels: 7
        0.84            0.14        0.02

Matches are distributed among these distances:
 156   52  0.20
 157  201  0.78
 158    6  0.02

ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30


Consensus pattern (158 bp):   
TGGTCTTGGATGTCCTACCGATGGCTGAGATCTTGCAATTGTTACAGATTCTCCACAGCTCGTGT
GAGTAGCATCGTGTAGCTTAACATCCCGACCCATAGCTCGTGTGAGTAGGCCCATTTCACAGATC
ATGTGAGCCATACAAGATATAAGAGTAC

Found at i:9556 original size:41 final size:41

Alignment explanation


    Indices: 9431--9561  Score: 174
    Period size: 41  Copynumber: 3.2  Consensus size: 41

       9421 ACAGAAAACG

                *                                   *
       9431 CCGCAAAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCG
          1 CCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCA

                    *    *                        *  
       9472 CCGCTAAAAGTCAAAGCAATAGCGACGCTTATGGAAAAACA
          1 CCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCA

                                      *     *   *     
       9513 CCGCTAAAGGTCAGAGCAATAGCGACACTTACAGG-CAAGCA
          1 CCGCTAAAGGTCAGAGCAATAGCGACGCTTA-TGGAAAAGCA

                    
       9554 CCGCTAAA
          1 CCGCTAAA

       9562 AATCAGTGCA


Statistics
Matches: 78,  Mismatches: 11, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  41   76  0.97
  42    2  0.03

ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13


Consensus pattern (41 bp):   
CCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCA

Found at i:9590 original size:24 final size:24

Alignment explanation


    Indices: 9554--9608  Score: 76
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       9544 CAGGCAAGCA

                                     
       9554 CCGCTAAAAATCAG-TGCATTAGCG
          1 CCGCTAAAAATCAGAT-CATTAGCG

                    *               
       9578 CCGCTAAAGATCAGATCATTAGCG
          1 CCGCTAAAAATCAGATCATTAGCG

            *      
       9602 ACGCTAA
          1 CCGCTAA

       9609 TTGGAAAAAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  24   27  0.96
  25    1  0.04

ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20


Consensus pattern (24 bp):   
CCGCTAAAAATCAGATCATTAGCG

Found at i:9729 original size:19 final size:19

Alignment explanation


    Indices: 9707--9749  Score: 59
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       9697 TTATATAAAC

                      *        
       9707 TAAAAAAATTCTAAAATTT
          1 TAAAAAAATTATAAAATTT

                   *    *      
       9726 TAAAAAATTTATTAAATTT
          1 TAAAAAAATTATAAAATTT

                 
       9745 TAAAA
          1 TAAAA

       9750 CTTATATAAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40


Consensus pattern (19 bp):   
TAAAAAAATTATAAAATTT
Done.