Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006742.1 Kokia drynarioides strain JFW-HI SEQ_121340, 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: 1974
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33


Found at i:1774 original size:42 final size:42

Alignment explanation


    Indices: 1715--1974  Score: 378
    Period size: 42  Copynumber: 6.1  Consensus size: 42

       1705 AAGGAAAACA

                                 *      *             
       1715 TTCATTGCATTTAGAGGCCCAGGTGTGGCGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

                               *    *                   
       1757 TTCATTGCATTTAGAGGCCTAAGTATGGAGG-CTCATTTACTTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTC-CATTTAC-TT

                              *  *                    
       1800 TTCATTGCATTTAGAGGCTCAGGTGTGGAGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

                                      *               
       1842 TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

                 *     *                    *          
       1884 TTCATCGCATTCAGAGGGCCCAAGTGTGGAGGCCCATTTACTT
          1 TTCATTGCATTTAGA-GGCCCAAGTGTGGAGGTCCATTTACTT

                  *              *                    
       1927 TTCATTTCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
          1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

                  
       1969 TTCATT
          1 TTCATT


Statistics
Matches: 194,  Mismatches: 20, Indels: 8
        0.87            0.09        0.04

Matches are distributed among these distances:
  41    1  0.01
  42  119  0.61
  43   73  0.38
  44    1  0.01

ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37


Consensus pattern (42 bp):   
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT

Found at i:1858 original size:85 final size:84

Alignment explanation


    Indices: 1715--1974  Score: 387
    Period size: 85  Copynumber: 3.1  Consensus size: 84

       1705 AAGGAAAACA

                                        *                                *   
       1715 TTCATTGCATTTAGAGGCCCAGGTGTGGCGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAAG
          1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG

             *                   
       1780 TATGGAGG-CTCATTTACTTT
         66 TGTGGAGGTC-CATTTAC-TT

                              *                                              
       1800 TTCATTGCATTTAGAGGCTCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
          1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG

               *               
       1865 TGTAGAGGTCCATTTACTT
         66 TGTGGAGGTCCATTTACTT

                 *     *          *         *                *              *
       1884 TTCATCGCATTCAGAGGGCCCAAGTGTGGAGGCCCATTTACTTTTCATTTCATTTAGAGGCCCAG
          1 TTCATTGCATTTAGA-GGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAA

                                
       1949 GTGTGGAGGTCCATTTACTT
         65 GTGTGGAGGTCCATTTACTT

                  
       1969 TTCATT
          1 TTCATT


Statistics
Matches: 159,  Mismatches: 14, Indels: 4
        0.90            0.08        0.02

Matches are distributed among these distances:
  84   15  0.09
  85  143  0.90
  86    1  0.01

ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37


Consensus pattern (84 bp):   
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
TGTGGAGGTCCATTTACTT

Found at i:1941 original size:127 final size:127

Alignment explanation


    Indices: 1715--1974  Score: 414
    Period size: 127  Copynumber: 2.0  Consensus size: 127

       1705 AAGGAAAACA

                                 *    * *                  *     *       *   
       1715 TTCATTGCATTTAGAGGCCCAGGTGTGGCGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAAG
          1 TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCATCGCATTCAGAGGCCCAAG

                     *                            *                       
       1780 TATGGAGGCTCATTTACTTTTTCATTGCATTTAGAGGCTCAGGTGTGGAGGTCCATTTACTT
         66 TATGGAGGCCCATTTACTTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT

                                                                             
       1842 TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCATCGCATTCAGAGGGCCCAA
          1 TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCATCGCATTCAGA-GGCCCAA

              *                        *                                   
       1907 GTGTGGAGGCCCATTTAC-TTTTCATTTCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
         65 GTATGGAGGCCCATTTACTTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT

                  
       1969 TTCATT
          1 TTCATT


Statistics
Matches: 122,  Mismatches: 10, Indels: 2
        0.91            0.07        0.01

Matches are distributed among these distances:
 127  100  0.82
 128   22  0.18

ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37


Consensus pattern (127 bp):   
TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCATCGCATTCAGAGGCCCAAG
TATGGAGGCCCATTTACTTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Done.