Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002040.1 Kokia drynarioides strain JFW-HI SEQ_113927, 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: 1920
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23


Found at i:939 original size:139 final size:139

Alignment explanation


    Indices: 543--915  Score: 613
    Period size: 139  Copynumber: 2.7  Consensus size: 139

        533 AAACGGTTAG

                 *           *                                         **    
        543 CTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAATGGAT
          1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT

                 *                    *                                      
        608 TGAAATAGTGATGGGATCATCTTCCTAATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
         66 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA

                     
        673 CGAGCAAAT
        131 CGAGCAAAT

               *      *                                                      
        682 CTTTCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
          1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT

                                                                             
        747 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
         66 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA

                     
        812 CGAGCAAAT
        131 CGAGCAAAT

                                                                          *  
        821 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
          1 CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT

               *     *  *                  
        886 TGAGACAGACGACGTGG-TCATCTTCCTGAT
         66 TGAAACAG-TGATG-GGATCATCTTCCTGAT

        916 AAGATACTAA


Statistics
Matches: 218,  Mismatches: 14, Indels: 3
        0.93            0.06        0.01

Matches are distributed among these distances:
 139  200  0.92
 140   16  0.07
 141    2  0.01

ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22


Consensus pattern (139 bp):   
CTTCCAGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
CGAGCAAAT

Found at i:1386 original size:17 final size:17

Alignment explanation


    Indices: 1358--1430  Score: 96
    Period size: 17  Copynumber: 4.4  Consensus size: 17

       1348 TTGGAAATTG

                             
       1358 AATTTA-TTTAAATTTA
          1 AATTTATTTTAAATTTA

             *               
       1374 AGTTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

                              
       1391 AATTT-TTTTGAAATTTA
          1 AATTTATTTT-AAATTTA

                    *    *   
       1408 AATTTATTATAAAATTA
          1 AATTTATTTTAAATTTA

                  
       1425 AATTTA
          1 AATTTA

       1431 GAAAGTGCAA


Statistics
Matches: 50,  Mismatches: 4, Indels: 5
        0.85            0.07        0.08

Matches are distributed among these distances:
  16    9  0.18
  17   38  0.76
  18    3  0.06

ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55


Consensus pattern (17 bp):   
AATTTATTTTAAATTTA

Found at i:1474 original size:30 final size:30

Alignment explanation


    Indices: 1438--1503  Score: 105
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       1428 TTAGAAAGTG

                      *    *           *  
       1438 CAATTACAGATGGCCTGAATACAAATGGCC
          1 CAATTACAGACGGCCCGAATACAAATGACC

                                          
       1468 CAATTACAGACGGCCCGAATACAAATGACC
          1 CAATTACAGACGGCCCGAATACAAATGACC

                  
       1498 CAATTA
          1 CAATTA

       1504 AAAACTACCC


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18


Consensus pattern (30 bp):   
CAATTACAGACGGCCCGAATACAAATGACC
Done.