Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003354.1 Kokia drynarioides strain JFW-HI SEQ_116072, 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: 2483
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37


Found at i:840 original size:41 final size:42

Alignment explanation


    Indices: 741--841  Score: 159
    Period size: 43  Copynumber: 2.4  Consensus size: 42

        731 AAAAAGTGCT

                  *                      *           * 
        741 GCTAAAAACCATGTTCTTTAGCGGCGCTTTTGAGGGAAGTGTC
          1 GCTAAAGACCATGTTCTTTAGCGGCGCTTGTGAGGGAAG-GCC

                                                      
        784 GCTAAAGACCATGTTCTTTAGCGGCGCTTGTGAGGGAA-GCC
          1 GCTAAAGACCATGTTCTTTAGCGGCGCTTGTGAGGGAAGGCC

                             
        825 GCTAAAGACCATGTTCT
          1 GCTAAAGACCATGTTCT

        842 ATAACGGAGT


Statistics
Matches: 55,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  41   19  0.35
  43   36  0.65

ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28


Consensus pattern (42 bp):   
GCTAAAGACCATGTTCTTTAGCGGCGCTTGTGAGGGAAGGCC

Found at i:1017 original size:43 final size:44

Alignment explanation


    Indices: 822--1047  Score: 319
    Period size: 44  Copynumber: 5.2  Consensus size: 44

        812 TGTGAGGGAA

                                   *                    
        822 GCCGCTAAAGACCATGTTCTATAACGGAGTTTTTCCTCATAAAC
          1 GCCGCTAAAGACCATGTTCTATAGCGGAGTTTTTCCTCATAAAC

               *                     *                  
        866 GCCACTAAAGACCATGTTCTATAGCAGAGTTTTTCCTCATAAAC
          1 GCCGCTAAAGACCATGTTCTATAGCGGAGTTTTTCCTCATAAAC

               *                  *  *                  
        910 GCCACTAAAGACCATGTTCTATTGCAGAGTTTTTCCTCATAAAC
          1 GCCGCTAAAGACCATGTTCTATAGCGGAGTTTTTCCTCATAAAC

                           *                * ****    * 
        954 GCCGCTAAAGACCATTTTCTATAGCGGAGTTTGTGGGAAT-AGC
          1 GCCGCTAAAGACCATGTTCTATAGCGGAGTTTTTCCTCATAAAC

                                                        
        997 GCCGCTAAAGACCATGTTCTATAGCGGAGTTTTTCCTCATAAAC
          1 GCCGCTAAAGACCATGTTCTATAGCGGAGTTTTTCCTCATAAAC

             *     
       1041 GTCGCTA
          1 GCCGCTA

       1048 TTTTTAGCAG


Statistics
Matches: 159,  Mismatches: 22, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
  43   36  0.23
  44  123  0.77

ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30


Consensus pattern (44 bp):   
GCCGCTAAAGACCATGTTCTATAGCGGAGTTTTTCCTCATAAAC

Found at i:1047 original size:87 final size:86

Alignment explanation


    Indices: 783--1047  Score: 327
    Period size: 88  Copynumber: 3.1  Consensus size: 86

        773 AGGGAAGTGT

                              *      * *        *                           *
        783 CGCTAAAGACCATGTTCTTTAGCGGCGCTTGTGAGGGA-A-GCCGCTAAAGACCATGTTCTATAA
          1 CGCTAAAGACCATGTTCTATAGCGGAGTTTGTG-GGAATACGCCGCTAAAGACCATGTTCTATAG

                                  
        846 CGGAGTTTTTCCTCATAAACGC
         65 CGGAGTTTTTCCTCATAAACGC

             *                     *      *  ***   *     *                  *
        868 CACTAAAGACCATGTTCTATAGCAGAGTTTTTCCTCATAAACGCCACTAAAGACCATGTTCTATT
          1 CGCTAAAGACCATGTTCTATAGCGGAGTTTGT-GGGA-ATACGCCGCTAAAGACCATGTTCTATA

              *                    
        933 GCAGAGTTTTTCCTCATAAACGC
         64 GCGGAGTTTTTCCTCATAAACGC

                         *                                                   
        956 CGCTAAAGACCATTTTCTATAGCGGAGTTTGTGGGAATAGCGCCGCTAAAGACCATGTTCTATAG
          1 CGCTAAAGACCATGTTCTATAGCGGAGTTTGTGGGAATA-CGCCGCTAAAGACCATGTTCTATAG

                                 *
       1021 CGGAGTTTTTCCTCATAAACGT
         65 CGGAGTTTTTCCTCATAAACGC

                 
       1043 CGCTA
          1 CGCTA

       1048 TTTTTAGCAG


Statistics
Matches: 149,  Mismatches: 26, Indels: 8
        0.81            0.14        0.04

Matches are distributed among these distances:
  85   26  0.17
  86    3  0.02
  87   50  0.34
  88   70  0.47

ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29


Consensus pattern (86 bp):   
CGCTAAAGACCATGTTCTATAGCGGAGTTTGTGGGAATACGCCGCTAAAGACCATGTTCTATAGC
GGAGTTTTTCCTCATAAACGC
Done.