Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013156.1 Kokia drynarioides strain JFW-HI SEQ_128175, 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, 811

Length: 1352
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37


Found at i:567 original size:42 final size:42

Alignment explanation


    Indices: 65--544  Score: 687
    Period size: 42  Copynumber: 11.4  Consensus size: 42

         55 AAGGAAAACA

                                                       
         65 TTCATTGCATTTAGAGGCCCAAGTGT-GACGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGA-GGTCCATTTACTT

                         *     *    *         *         
        107 TTCATTGCATTTAAAGGCCTAAGTATGGAGG-CTTATTTACTTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTC-CATTTAC-TT

                                 *                    
        150 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

                                      *               
        192 TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

                 *     *                    *          
        234 TTCATCGCATTCAGAGGGCCCAAGTGTGGAGGCCCATTTACTT
          1 TTCATTGCATTTAGA-GGCCCAAGTGTGGAGGTCCATTTACTT

                  *              *                    
        277 TTCATTTCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

                                                      
        319 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

                                                      
        361 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

                         *       *    **              
        403 TTCATTGCATTTAAAGGCCCAGGTGTAAAGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

              *                            *        * 
        445 TTTATTGCATTTAGAGGCCCAAGTGTGGAGGCCCATTTACCT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

               *                *         *  *         
        487 TTCGTTGCATTTA-AGGGCCTAAGTGTGGATGTTCATTTACTT
          1 TTCATTGCATTTAGA-GGCCCAAGTGTGGAGGTCCATTTACTT

                     *      
        529 TTCATTGCAATTAGAG
          1 TTCATTGCATTTAGAG

        545 TCCTAAGCAT


Statistics
Matches: 389,  Mismatches: 42, Indels: 14
        0.87            0.09        0.03

Matches are distributed among these distances:
  41    2  0.01
  42  311  0.80
  43   75  0.19
  44    1  0.00

ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36


Consensus pattern (42 bp):   
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

Found at i:571 original size:4 final size:4

Alignment explanation


    Indices: 562--596  Score: 56
    Period size: 4  Copynumber: 9.2  Consensus size: 4

        552 CATAGAGGTC

                                                          
        562 TATT TATT TATT TATT TA-T T-TT TATT TATT TATT T
          1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T

        597 CATTGTATAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   3    4  0.14
   4   25  0.86

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (4 bp):   
TATT

Found at i:587 original size:14 final size:14

Alignment explanation


    Indices: 568--596  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

        558 GGTCTATTTA

                          
        568 TTTATTTATTTATT
          1 TTTATTTATTTATT

                          
        582 TTTATTTATTTATT
          1 TTTATTTATTTATT

             
        596 T
          1 T

        597 CATTGTATAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79


Consensus pattern (14 bp):   
TTTATTTATTTATT
Done.