Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004659.1 Kokia drynarioides strain JFW-HI SEQ_118200, 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: 9437
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Found at i:55 original size:26 final size:26

Alignment explanation


    Indices: 4--73  Score: 63
    Period size: 26  Copynumber: 2.6  Consensus size: 26

          1 ACT

                           *            
          4 ATATATAAAATTTCAATAAAT-AAAA-A
          1 ATATATAAAA-TT-ATTAAATAAAAATA

                                        
         30 ATATATAAAATTATTAAATATTAAAATA
          1 ATATATAAAATTATTAAATA--AAAATA

                    *       
         58 ATATAATATAATTATT
          1 ATAT-ATAAAATTATT

         74 TTTAAATAAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 7
        0.80            0.04        0.15

Matches are distributed among these distances:
  24    6  0.16
  25    2  0.05
  26   10  0.27
  27    4  0.11
  28    5  0.14
  29   10  0.27

ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39


Consensus pattern (26 bp):   
ATATATAAAATTATTAAATAAAAATA

Found at i:8056 original size:51 final size:51

Alignment explanation


    Indices: 7937--8174  Score: 300
    Period size: 51  Copynumber: 4.6  Consensus size: 51

       7927 TTTCATTTGA

                                   * *        **   *  *          *
       7937 TACTCACGATGACA-TATAGTCACCGGACCTCTTGTTCCATATAGGAATTCATA
          1 TACTCACGATGACACT-TAGTCATCAGACCT-TTAATCCGTAAAGG-ATTCATT

                            *                    * * *         
       7990 TACTCACGATGACACTGAGTCATCAGACCTTTAATCCATCATGGATTCATT
          1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT

                  *                 *                          
       8041 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
          1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT

                        *                                      
       8092 TACTCACGATGATACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
          1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT

                                             
       8143 TACTCACGATGACACTTAGTCATC-GAACCTTT
          1 TACTCACGATGACACTTAGTCATCAG-ACCTTT

       8175 TCGTTTATAG


Statistics
Matches: 164,  Mismatches: 19, Indels: 6
        0.87            0.10        0.03

Matches are distributed among these distances:
  50    1  0.01
  51  128  0.78
  52    9  0.05
  53   25  0.15
  54    1  0.01

ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32


Consensus pattern (51 bp):   
TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT

Found at i:8945 original size:3 final size:3

Alignment explanation


    Indices: 8937--8969  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       8927 TTGGCCGTGT

                                                       
       8937 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA

       8970 AACATGTGAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
GAA

Done.