Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009503.1 Kokia drynarioides strain JFW-HI SEQ_124214, 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: 17989
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34


Found at i:69 original size:29 final size:30

Alignment explanation


    Indices: 1--201  Score: 214
    Period size: 29  Copynumber: 6.8  Consensus size: 30

                     **    *        *    *
          1 TAAACTTTTATAAAAATACATTTTTACCCT
          1 TAAACTTTTCCAAAATTACATTTTAACCCC

              *                     *     
         31 TATACTTTTCCAAAATTACATTTTGACCCC
          1 TAAACTTTTCCAAAATTACATTTTAACCCC

                                           
         61 TAAAC-TTTCCAAAATTACATTTTGAA-CCC
          1 TAAACTTTTCCAAAATTACATTTT-AACCCC

                                           
         90 T--ACTCTTTCCAAAATTACATTTTAACCCC
          1 TAAACT-TTTCCAAAATTACATTTTAACCCC

                                          
        119 TAAACTTTTCCAAAA-TACATTTTAACCCC
          1 TAAACTTTTCCAAAATTACATTTTAACCCC

             * **           *             
        148 TGATTTTTTCCAAAATCACATTTTAACCCC
          1 TAAACTTTTCCAAAATTACATTTTAACCCC

            ** *             *      
        178 CGAGCTTTTCCAAAATTTCATTTT
          1 TAAACTTTTCCAAAATTACATTTT

        202 CATCTAAAGT


Statistics
Matches: 147,  Mismatches: 17, Indels: 14
        0.83            0.10        0.08

Matches are distributed among these distances:
  27    2  0.01
  28    2  0.01
  29   70  0.48
  30   70  0.48
  31    3  0.02

ACGTcount: A:0.33, C:0.25, G:0.02, T:0.39


Consensus pattern (30 bp):   
TAAACTTTTCCAAAATTACATTTTAACCCC

Found at i:162 original size:59 final size:57

Alignment explanation


    Indices: 13--193  Score: 220
    Period size: 59  Copynumber: 3.1  Consensus size: 57

          3 AACTTTTATA

                        *         *                   *                
         13 AAAATACATTTTTACCCTTATACTTTTCCAAAATTACATTTTGACCCCTAAAC-TTTCC
          1 AAAATACATTTTAACCC-TAT-TTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCC

                                 * *                                   
         71 AAAATTACATTTTGAACCCTACTCTTTCCAAAATTACATTTTAACCCCTAAACTTTTCC
          1 AAAA-TACATTTT-AACCCTATTTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCC

                                              *             ** *       
        130 AAAATACATTTTAACCCCTGATTTTTTCCAAAATCACATTTTAACCCCCGAGCTTTTCC
          1 AAAATACATTTTAA-CCCT-ATTTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCC

                 
        189 AAAAT
          1 AAAAT

        194 TTCATTTTCA


Statistics
Matches: 107,  Mismatches: 11, Indels: 9
        0.84            0.09        0.07

Matches are distributed among these distances:
  57    2  0.02
  58   44  0.41
  59   57  0.53
  60    4  0.04

ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37


Consensus pattern (57 bp):   
AAAATACATTTTAACCCTATTTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCC

Found at i:10884 original size:18 final size:18

Alignment explanation


    Indices: 10846--10899  Score: 63
    Period size: 18  Copynumber: 3.0  Consensus size: 18

      10836 TTATATTTTT

                      *     * 
      10846 ATAATATTAAATAATAAA
          1 ATAATATTAATTAATATA

               *    *    *    
      10864 ATATTATTTATTATTATA
          1 ATAATATTAATTAATATA

                              
      10882 ATAATATTAATTAATATA
          1 ATAATATTAATTAATATA

      10900 TCTTTTGATA


Statistics
Matches: 28,  Mismatches: 8, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  18   28  1.00

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (18 bp):   
ATAATATTAATTAATATA
Done.