Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009599.1 Kokia drynarioides strain JFW-HI SEQ_124315, 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: 3223
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34

Warning! 3 characters in sequence are not A, C, G, or T


Found at i:103 original size:45 final size:45

Alignment explanation


    Indices: 36--172  Score: 184
    Period size: 45  Copynumber: 3.0  Consensus size: 45

         26 GCATAGCTCA

                             *                         * 
         36 TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGCAATGC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

                *                  *                     
         81 TCAAACCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

                 **           *  *              *   *    
        126 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCATCGCGATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

              
        171 TC
          1 TC

        173 TATTCCTCCC


Statistics
Matches: 80,  Mismatches: 12, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  45   80  1.00

ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

Found at i:193 original size:21 final size:21

Alignment explanation


    Indices: 167--209  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        157 AGCCATCGCG

                    *            
        167 ATACTCTATTCCTCCCGGGCA
          1 ATACTCTACTCCTCCCGGGCA

                           *     
        188 ATACTCTACTCCTCCGGGGCA
          1 ATACTCTACTCCTCCCGGGCA

             
        209 A
          1 A

        210 ATGGACCCTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26


Consensus pattern (21 bp):   
ATACTCTACTCCTCCCGGGCA

Found at i:2649 original size:54 final size:54

Alignment explanation


    Indices: 2591--2693  Score: 129
    Period size: 54  Copynumber: 1.9  Consensus size: 54

       2581 TAACTAAATA

                     *                                              
       2591 AAAAAAATGGTAAA-AACAAAGACATGAATTGCAAAAATTA-GGTGATGTGATTTC
          1 AAAAAAATGCTAAAGAACAAA-ACATGAATTGCAAAAATTACGG-GATGTGATTTC

                 *         **                *               
       2645 AAAAAGATGCTAAAGGGCAAAACATGAATTGCATAAATTACGGGATGTG
          1 AAAAAAATGCTAAAGAACAAAACATGAATTGCAAAAATTACGGGATGTG

       2694 GGTTGAAAAA


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  54   36  0.86
  55    6  0.14

ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22


Consensus pattern (54 bp):   
AAAAAAATGCTAAAGAACAAAACATGAATTGCAAAAATTACGGGATGTGATTTC
Done.