Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014202.1 Kokia drynarioides strain JFW-HI SEQ_129235, 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: 2264
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24


Found at i:1073 original size:139 final size:139

Alignment explanation


    Indices: 327--1069  Score: 1236
    Period size: 139  Copynumber: 5.3  Consensus size: 139

        317 AAACAGTTAG

                 *    *      *                              *       *  *     
        327 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAAAAACGGAT
          1 CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGAT

                                                                             
        392 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAA
         66 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAA

                     
        457 CGAGCAAAT
        131 CGAGCAAAT

                                                     *                    *  
        466 CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCTTGATGAAATACAGAGAAGCGAAT
          1 CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGAT

                                              *                              
        531 TGAAACAGTGATGGGATCATCTTCCTGATGAGACGCTGAGAAGAAAACCCAAACGAGGCTCGAAA
         66 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAA

             *       
        596 CAAGCAAAT
        131 CGAGCAAAT

                                                                             
        605 CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGAT
          1 CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGAT

                                              *          *                   
        670 TGAAACAGTGATGGGATCATCTTCCTGATGAGACGCTGAGAAGAAGACCCAAACGAGGCTCGAAA
         66 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAA

               *     
        735 CGAACAAAT
        131 CGAGCAAAT

                    *                                                   *    
        744 CTTCCAGACGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGTGGAT
          1 CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGAT

                          *  *                           *                   
        809 TGAAACAGTGATGGAATAATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
         66 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAA

                     
        874 CGAGCAAAT
        131 CGAGCAAAT

                             *          *                   *            *   
        883 CTTCCAGATGGGATACTGAGAAGTGAACAAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGAT
          1 CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGAT

                                               *         *                   
        948 TGAAACAGTGATGGGATCATCTTCCTGATGAGACATTGAGAAGAATACCCAAACGAGGCTCGAAA
         66 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAA

                  *  
       1013 CGAGCAGAT
        131 CGAGCAAAT

                              *                              
       1022 CTTCCAGATGAGG-TACTGAGAAGTGAACCAAATTCGTCTTCCTGATGA
          1 CTTCCAGATG-GGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGA

       1070 GATAAGCGAA


Statistics
Matches: 570,  Mismatches: 33, Indels: 2
        0.94            0.05        0.00

Matches are distributed among these distances:
 139  568  1.00
 140    2  0.00

ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20


Consensus pattern (139 bp):   
CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCGGAT
TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAA
CGAGCAAAT

Found at i:1619 original size:17 final size:17

Alignment explanation


    Indices: 1591--1646  Score: 78
    Period size: 17  Copynumber: 3.4  Consensus size: 17

       1581 TTGGAAATTG

                             
       1591 AATTTA-TTTAAATTTA
          1 AATTTATTTTAAATTTA

             *               
       1607 AGTTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

                    *    *   
       1624 AATTTATTATAAAATTA
          1 AATTTATTTTAAATTTA

                  
       1641 AATTTA
          1 AATTTA

       1647 AAAAGTCCAA


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  16    5  0.14
  17   30  0.86

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54


Consensus pattern (17 bp):   
AATTTATTTTAAATTTA

Found at i:1689 original size:15 final size:15

Alignment explanation


    Indices: 1665--1705  Score: 73
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1655 AAAACAAAGT

                           
       1665 CCAATTACAAATGGC
          1 CCAATTACAAATGGC

                 *         
       1680 CCAATAACAAATGGC
          1 CCAATTACAAATGGC

                       
       1695 CCAATTACAAA
          1 CCAATTACAAA

       1706 CTACCCAAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  15   24  1.00

ACGTcount: A:0.46, C:0.27, G:0.10, T:0.17


Consensus pattern (15 bp):   
CCAATTACAAATGGC
Done.