Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000477.1 Kokia drynarioides strain JFW-HI SEQ_111352, 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: 4385
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:147 original size:27 final size:28

Alignment explanation


    Indices: 89--154  Score: 71
    Period size: 27  Copynumber: 2.4  Consensus size: 28

         79 TCATAATTTT

                      *                *
         89 ATATTATATTCATTTCAAAATATAATTT
          1 ATATTATATTAATTTCAAAATATAATTC

                             * *    *   
        117 ATATTATATTAATTTC-CATTATACTTC
          1 ATATTATATTAATTTCAAAATATAATTC

                *      
        144 ATATAATATTA
          1 ATATTATATTA

        155 TGTTTGCATT


Statistics
Matches: 32,  Mismatches: 6, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  27   17  0.53
  28   15  0.47

ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50


Consensus pattern (28 bp):   
ATATTATATTAATTTCAAAATATAATTC

Found at i:4145 original size:17 final size:17

Alignment explanation


    Indices: 4123--4185  Score: 90
    Period size: 17  Copynumber: 3.7  Consensus size: 17

       4113 TTGGAAATTG

                   *         
       4123 AATTTAAGTTTATTTTA
          1 AATTTAAATTTATTTTA

                           * 
       4140 AATTTAAATTTATTTGA
          1 AATTTAAATTTATTTTA

                          *  
       4157 AATTTAAATTTATTATA
          1 AATTTAAATTTATTTTA

              *         
       4174 AAATTAAATTTA
          1 AATTTAAATTTA

       4186 GAAAAGTCCG


Statistics
Matches: 41,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   41  1.00

ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52


Consensus pattern (17 bp):   
AATTTAAATTTATTTTA

Found at i:4247 original size:15 final size:15

Alignment explanation


    Indices: 4210--4252  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       4200 CAAAAAAAAT

                           
       4210 CCAAA-ACAAATGGC
          1 CCAAATACAAATGGC

               **    *     
       4224 CCAGTTACAGATGGC
          1 CCAAATACAAATGGC

                          
       4239 CCAAATACAAATGG
          1 CCAAATACAAATGG

       4253 TCTAATTATA


Statistics
Matches: 22,  Mismatches: 6, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  14    3  0.14
  15   19  0.86

ACGTcount: A:0.42, C:0.26, G:0.19, T:0.14


Consensus pattern (15 bp):   
CCAAATACAAATGGC
Done.