Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007146.1 Kokia drynarioides strain JFW-HI SEQ_121758, 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: 16865
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33


Found at i:1994 original size:93 final size:93

Alignment explanation


    Indices: 1527--1972  Score: 732
    Period size: 93  Copynumber: 4.8  Consensus size: 93

       1517 TGATTGTCCA

                       *          *         *        * *                   * 
       1527 CCAACATTCTCTACATCTCTTGTGATGGAAATCATAGGCAAGGTATTTACCCCACAAG-AGCTAT
          1 CCAACATTCTCCACATCTCTTGGGATGGAAATTATAGGCAAAGCATTTACCCCACAAGCA-CTCT

               * *         *             
       1591 CTTTAGTTTGTATCAAGGCAGTCTTTTCT
         65 CTTCATTTTGTATCAGGGCAGTCTTTTCT

                                    *                                        
       1620 CCAACATTCTCCACATCTCTTGGGTTGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTCTC
          1 CCAACATTCTCCACATCTCTTGGGATGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTCTC

                                        
       1685 TTCATTTTGTATCAGGGCAGTCTTTTCT
         66 TTCATTTTGTATCAGGGCAGTCTTTTCT

                                *   *                                        
       1713 CCAACATTCTCCACATCTCTCGGGTTGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTCTC
          1 CCAACATTCTCCACATCTCTTGGGATGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTCTC

                                        
       1778 TTCATTTTGTATCAGGGCAGTCTTTTCT
         66 TTCATTTTGTATCAGGGCAGTCTTTTCT

                        *                                                    
       1806 CCAACATTCTCCGCATCTCTTGGGATGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTCTC
          1 CCAACATTCTCCACATCTCTTGGGATGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTCTC

                                        
       1871 TTCATTTTGTATCAGGGCAGTCTTTTCT
         66 TTCATTTTGTATCAGGGCAGTCTTTTCT

                          *                 *                             *  
       1899 CCAACATTCTCCACGTCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTATC
          1 CCAACATTCTCCACATCTCTTGGGATGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTCTC

                     
       1964 TTCATTTTG
         66 TTCATTTTG

       1973 CACTGGGCCA


Statistics
Matches: 334,  Mismatches: 18, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
  93  333  1.00
  94    1  0.00

ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32


Consensus pattern (93 bp):   
CCAACATTCTCCACATCTCTTGGGATGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTCTC
TTCATTTTGTATCAGGGCAGTCTTTTCT

Found at i:5004 original size:21 final size:20

Alignment explanation


    Indices: 4980--5028  Score: 53
    Period size: 21  Copynumber: 2.4  Consensus size: 20

       4970 TTGGTTATTT

                                 
       4980 AAAATAAAAAATAAATTATAA
          1 AAAATAAAAAA-AAATTATAA

                    *        * * 
       5001 AAAATTAACAAAAAATTGTGA
          1 AAAA-TAAAAAAAAATTATAA

                   
       5022 AAAATAA
          1 AAAATAA

       5029 TAAGTAAAAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  20    3  0.12
  21   15  0.62
  22    6  0.25

ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22


Consensus pattern (20 bp):   
AAAATAAAAAAAAATTATAA

Found at i:15641 original size:20 final size:20

Alignment explanation


    Indices: 15616--15667  Score: 77
    Period size: 20  Copynumber: 2.6  Consensus size: 20

      15606 AGTCATCAAG

                                
      15616 GTATCGGTAGAACTGGAGTT
          1 GTATCGGTAGAACTGGAGTT

                        *       
      15636 GTATCGGTAGAAGTGGAGTT
          1 GTATCGGTAGAACTGGAGTT

            *  *        
      15656 CTACCGGTAGAA
          1 GTATCGGTAGAA

      15668 GTCTCACTGG


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   29  1.00

ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27


Consensus pattern (20 bp):   
GTATCGGTAGAACTGGAGTT

Done.