Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010087.1 Kokia drynarioides strain JFW-HI SEQ_124868, 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: 3827
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.37

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:1305 original size:3 final size:3

Alignment explanation


    Indices: 1280--1355  Score: 127
    Period size: 3  Copynumber: 25.7  Consensus size: 3

       1270 CAACTTTTTT

                          *       *                                        
       1280 TTA TT- TTA TTG TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                                                  
       1327 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       1356 GTTAATAATA


Statistics
Matches: 68,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
   2    2  0.03
   3   66  0.97

ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:2157 original size:11 final size:10

Alignment explanation


    Indices: 2121--2178  Score: 59
    Period size: 10  Copynumber: 5.8  Consensus size: 10

       2111 ATTGGACATT

                      
       2121 AATTTAAATA
          1 AATTTAAATA

                        
       2131 AATTTAAACTTA
          1 AATTTAAA--TA

                       
       2143 AATTTATAATA
          1 AATTTA-AATA

                      
       2154 AATTTAAAT-
          1 AATTTAAATA

                   *  
       2163 --TTTAAGTA
          1 AATTTAAATA

                    
       2171 AATTTAAA
          1 AATTTAAA

       2179 CTTAAAATAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 12
        0.74            0.04        0.22

Matches are distributed among these distances:
   7    6  0.15
  10   16  0.40
  11    8  0.20
  12    8  0.20
  13    2  0.05

ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43


Consensus pattern (10 bp):   
AATTTAAATA

Found at i:2160 original size:17 final size:17

Alignment explanation


    Indices: 2135--2213  Score: 104
    Period size: 17  Copynumber: 4.6  Consensus size: 17

       2125 TAAATAAATT

                *         *  
       2135 TAAACTTAAATTTATAA
          1 TAAATTTAAATTTAAAA

                         *  *
       2152 TAAATTTAAATTTTAAG
          1 TAAATTTAAATTTAAAA

                      *      
       2169 TAAATTTAAACTTAAAA
          1 TAAATTTAAATTTAAAA

                     *       
       2186 TAAATTTAATTTTAAAA
          1 TAAATTTAAATTTAAAA

                       
       2203 TAAATTTAAAT
          1 TAAATTTAAAT

       2214 CCTGTTGGAC


Statistics
Matches: 52,  Mismatches: 10, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  17   52  1.00

ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43


Consensus pattern (17 bp):   
TAAATTTAAATTTAAAA

Done.