Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003641.1 Kokia drynarioides strain JFW-HI SEQ_116540, 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, 897

Length: 1496
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26


Found at i:197 original size:32 final size:33

Alignment explanation


    Indices: 132--197  Score: 80
    Period size: 37  Copynumber: 1.9  Consensus size: 33

        122 AATCGGTTAC

                             *                   
        132 CTTCCTGATGAGATACAGAGAAGTGAACCGGATCCGT
          1 CTTCCTGATGAGATACAAAGAAGT--A--GGATCCGT

                                          
        169 CTTCCTGATGAGATACAAAGAAGT-GGATC
          1 CTTCCTGATGAGATACAAAGAAGTAGGATC

        198 AAAATAGAGA


Statistics
Matches: 28,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  32    5  0.18
  37   23  0.82

ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23


Consensus pattern (33 bp):   
CTTCCTGATGAGATACAAAGAAGTAGGATCCGT

Found at i:365 original size:209 final size:208

Alignment explanation


    Indices: 1--667  Score: 917
    Period size: 209  Copynumber: 3.2  Consensus size: 208

                                              *     * *      *       *       
          1 GCGGTCATCTTCCTGATGAGATA-TAGAGAAGTACACCAACTTAATGAAACAAAGCTTGATGTGA
          1 GCGGTCATCTTCCTGATGAGATACT-GAGAAGTAGACCAAATCAATGAAGCAAAGCTCGATGTGA

                 *                              *        *             *     
         65 GTGAAACTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGATCGAAGCAATAAATCGGTT
         65 GTGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGGTT

                                          *                                  
        130 ACCTTCCTGATGAGATACAGAGAAGTGAACCGGATCCGTCTTCCTGATGAGATACAAAGAAGTGG
        130 ACCTTCCTGATGAGATACAGAGAAGTGAACTGGATCCGTCTTCCTGATGAGATACAAAGAAGTGG

                   *      
        195 ATCAAAATAGAGAT
        195 ATCAAAAAAGAGAT

                                                                             
        209 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCGAAAGCTCGATGTGA
          1 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGC-AAAGCTCGATGTGA

                     *        *   ** *              * *                  *   
        274 GTGAATCTTTGAACCCCATCTTTTTTATGAGATACTAAGATGTAGGTCGAAGCAATAAAACTGTT
         65 GTGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGGTT

                       *       *                                    *        
        339 ACCTTCCTGATTAGATACAAAGAAGTGAACTGGATCCGTCTTCCTGATGAGATACAGAGAAGTGG
        130 ACCTTCCTGATGAGATACAGAGAAGTGAACTGGATCCGTCTTCCTGATGAGATACAAAGAAGTGG

                           
        404 ATCAAAACAA-AGAT
        195 ATCAAAA-AAGAGAT

                 *                   * *                 *            *      
        418 GCGGTTATCTTCCTGATGAGATACTAATAAGTAGACCAAATCAATTAAGCCAAAGCTCAATGTGA
          1 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAG-CAAAGCTCGATGTGA

             *                                              *          *     
        483 GCGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAA-AAGCAGGTCAAAGCAATAAAGCGGTT
         65 GTGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGGTT

                                           *     *     *        *   *        
        547 ACCTTCCTGATGAGATACAGAGAAGTGAACTAGATCCTTCTTCTTGATGAGACACATAGAAGTGG
        130 ACCTTCCTGATGAGATACAGAGAAGTGAACTGGATCCGTCTTCCTGATGAGATACAAAGAAGTGG

                       *   
        612 ATCAAAACAAGTGAT
        195 ATCAAAA-AAGAGAT

              *        *           *                 
        627 GCAGTCATCTTGCTGATGAGATATTGAGAAGTAGACCAAAT
          1 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAAT

        668 AAATAACACC


Statistics
Matches: 402,  Mismatches: 52, Indels: 9
        0.87            0.11        0.02

Matches are distributed among these distances:
 208  133  0.33
 209  267  0.66
 210    2  0.00

ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24


Consensus pattern (208 bp):   
GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCAAAGCTCGATGTGAG
TGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGGTTA
CCTTCCTGATGAGATACAGAGAAGTGAACTGGATCCGTCTTCCTGATGAGATACAAAGAAGTGGA
TCAAAAAAGAGAT
Done.