Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011190.1 Kokia drynarioides strain JFW-HI SEQ_126166, 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, 602

Length: 1004
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35


Found at i:150 original size:41 final size:41

Alignment explanation


    Indices: 88--388  Score: 404
    Period size: 41  Copynumber: 7.3  Consensus size: 41

         78 ACTTGACGTA

                          *                           
         88 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
          1 TAAA-GGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

                        *                    *       
        130 TAAAGGAAGACTTGTGTCTCGAGATGAGCATGATATTATAT
          1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

                            *     *          *       
        171 TAAAGGAAGACTCGTGACTCGAAATGAGCATGAAATTATAT
          1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

                   *        *     *                  
        212 TAAAGGAGGACTCGTGACTCGAAATGAGCATGAGATTATAT
          1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

                               * * *                 
        253 TAAAGGAAGACTCGTGTCTTGGGGTGAGCATGAGATTATAT
          1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

                *   *    *       * * *               
        294 TAAAAGAATACTCATGTCTCGGGGTAAGCATGAGATTATAT
          1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

                            *    *                    
        335 TAAAGGAAGACTCGTGACTCGGGATGAGCATGAGATTATATT
          1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATA-T

                        
        377 TAAAGGAAGACT
          1 TAAAGGAAGACT

        389 TATGACTCGG


Statistics
Matches: 232,  Mismatches: 26, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
  41  215  0.93
  42   17  0.07

ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27


Consensus pattern (41 bp):   
TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

Found at i:405 original size:123 final size:122

Alignment explanation


    Indices: 88--426  Score: 405
    Period size: 123  Copynumber: 2.7  Consensus size: 122

         78 ACTTGACGTA

                          *  *                                               
         88 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAAGGAAGACTTGTGTCTCGAG
          1 TAAA-GGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTTGTGTCTCG-G

                       *           *   *    *           *               
        153 -ATGAGCATGATATTATATTAAAGGAAGACTCGTGACTCGAAATGAGCATGAAATTATAT
         64 TA-GAGCATGAGATTATATTAAAAGAATACTCATGACTCGAAATAAGCATGAAATTATAT

                   *              *                              *        *  
        212 TAAAGGAGGACTCGTGACTCGAAATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTTGGGG
          1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTTGTGTC-T-CGG

                                              *    ***         *       
        277 T-GAGCATGAGATTATATTAAAAGAATACTCATGTCTCGGGGTAAGCATGAGATTATAT
         64 TAGAGCATGAGATTATATTAAAAGAATACTCATGACTCGAAATAAGCATGAAATTATAT

                                 *                                 *  *      
        335 TAAAGGAAGACTCGTGACTCGGGATGAGCATGAGATTATATTTAAAGGAAGACTTATGACTCGGT
          1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATA-TTAAAGGAAGACTTGTGTCTCGGT

                   *     *              
        400 AGAGCATAAGATTGT-TTAAAAGGAATA
         65 AGAGCATGAGATTATATTAAAA-GAATA

        427 TCTACGACTC


Statistics
Matches: 184,  Mismatches: 25, Indels: 13
        0.83            0.11        0.06

Matches are distributed among these distances:
 122    9  0.05
 123  152  0.83
 124   22  0.12
 125    1  0.01

ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27


Consensus pattern (122 bp):   
TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTTGTGTCTCGGTA
GAGCATGAGATTATATTAAAAGAATACTCATGACTCGAAATAAGCATGAAATTATAT

Done.