Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003728.1 Kokia drynarioides strain JFW-HI SEQ_116685, 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: 5033
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34


Found at i:105 original size:31 final size:30

Alignment explanation


    Indices: 1--113  Score: 99
    Period size: 29  Copynumber: 3.7  Consensus size: 30

                                            
          1 AACCTTCCAAAATT-CCATTTTTTTGACCTCA
          1 AACCTTCCAAAATTACCA--TTTTTGACCTCA

              **                           
         32 AATTTTCCAAAATTACCA-TTTT-ACCCTCA
          1 AACCTTCCAAAATTACCATTTTTGA-CCTCA

            * **   *                       
         61 GATGTTCAAAAATT-CCATTTTTGACCTCGA
          1 AACCTTCCAAAATTACCATTTTTGACCTC-A

                                   
         91 AACCTTCCAAAAATTACCATTTT
          1 AACCTTCC-AAAATTACCATTTT

        114 ACCCTCGGGC


Statistics
Matches: 66,  Mismatches: 9, Indels: 13
        0.75            0.10        0.15

Matches are distributed among these distances:
  28    4  0.06
  29   28  0.42
  30    6  0.09
  31   18  0.27
  32   10  0.15

ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37


Consensus pattern (30 bp):   
AACCTTCCAAAATTACCATTTTTGACCTCA

Found at i:120 original size:31 final size:31

Alignment explanation


    Indices: 36--120  Score: 90
    Period size: 31  Copynumber: 2.8  Consensus size: 31

         26 ACCTCAAATT

                                       * **
         36 TTCC-AAAATTACCATTTTACCCTC-AGATG
          1 TTCCAAAAATTACCATTTTACCCTCGAAACC

                                             
         65 TT-CAAAAATT-CCATTTTTGA-CCTCGAAACC
          1 TTCCAAAAATTACCA-TTTT-ACCCTCGAAACC

                                      
         95 TTCCAAAAATTACCATTTTACCCTCG
          1 TTCCAAAAATTACCATTTTACCCTCG

        121 GGCATCCAAA


Statistics
Matches: 46,  Mismatches: 3, Indels: 12
        0.75            0.05        0.20

Matches are distributed among these distances:
  28    4  0.09
  29   16  0.35
  30    6  0.13
  31   17  0.37
  32    3  0.07

ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34


Consensus pattern (31 bp):   
TTCCAAAAATTACCATTTTACCCTCGAAACC

Found at i:131 original size:60 final size:58

Alignment explanation


    Indices: 9--145  Score: 159
    Period size: 60  Copynumber: 2.3  Consensus size: 58

          1 AACCTTCC

                                     **                           ** *  
          9 AAAATTCCATTTTTTTGACCTCAAATTTTCCAAAATTACCATTTTACCCTCAGATGTTCA
          1 AAAATTCCA--TTTTTGACCTCAAACCTTCCAAAATTACCATTTTACCCTCAGACATCCA

                                                               * *      
         69 AAAATTCCATTTTTGACCTCGAAACCTTCCAAAAATTACCATTTTACCCTCGGGCATCCA
          1 AAAATTCCATTTTTGACCTC-AAACCTTCC-AAAATTACCATTTTACCCTCAGACATCCA

                              
        129 AAAA-TCACATTTTTGAC
          1 AAAATTC-CATTTTTGAC

        146 TCCATTTATT


Statistics
Matches: 67,  Mismatches: 7, Indels: 6
        0.84            0.09        0.08

Matches are distributed among these distances:
  58   11  0.16
  59    9  0.13
  60   47  0.70

ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35


Consensus pattern (58 bp):   
AAAATTCCATTTTTGACCTCAAACCTTCCAAAATTACCATTTTACCCTCAGACATCCA
Done.