Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012056.1 Kokia drynarioides strain JFW-HI SEQ_127054, 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: 13472
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:4351 original size:24 final size:24

Alignment explanation


    Indices: 4324--4400  Score: 79
    Period size: 24  Copynumber: 3.2  Consensus size: 24

       4314 TCCGCGTACC

                                   *
       4324 TAAAATATAAAAAATAAAAATAAG
          1 TAAAATATAAAAAATAAAAATAAA

                            *        
       4348 TAAAA-ATAAAATAATCAAAATAAA
          1 TAAAATATAAAA-AATAAAAATAAA

                     *                
       4372 T-AAATGATGAAAAAT-AAAATAGAA
          1 TAAAAT-ATAAAAAATAAAAATA-AA

                 
       4396 TAAAA
          1 TAAAA

       4401 AAAAATGGTT


Statistics
Matches: 45,  Mismatches: 3, Indels: 9
        0.79            0.05        0.16

Matches are distributed among these distances:
  23   15  0.33
  24   22  0.49
  25    8  0.18

ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21


Consensus pattern (24 bp):   
TAAAATATAAAAAATAAAAATAAA

Found at i:12138 original size:30 final size:30

Alignment explanation


    Indices: 12104--12390  Score: 286
    Period size: 30  Copynumber: 9.7  Consensus size: 30

      12094 GGGAAAATTC

                                          
      12104 AGGGTCAAAAATGGGATTTTTAGAAGTTTG
          1 AGGGTCAAAAATGGGATTTTTAGAAGTTTG

                          *      *         
      12134 AGGGT-AAAAATGGTATTTTTTGAAGTTTTG
          1 AGGGTCAAAAATGGGATTTTTAGAAG-TTTG

                 *       *                 
      12164 -GGGTTAAAAATGAGATTTTTTAGAAGTTTG
          1 AGGGTCAAAAATGGGA-TTTTTAGAAGTTTG

                                 *         
      12194 AGGGT-AAAAATGGGATTTTTGGAAGTTTCG
          1 AGGGTCAAAAATGGGATTTTTAGAAGTTT-G

                                         *
      12224 A-GGTCAAAAATGGGATTTTTAGAAG-TTC
          1 AGGGTCAAAAATGGGATTTTTAGAAGTTTG

             *          *        *  *      
      12252 AAGGTCAAAAATAGGATTTTTGGATGTTTTG
          1 AGGGTCAAAAATGGGATTTTTAGAAG-TTTG

                      *                   
      12283 -GGGTCAAAATTGGGATTTTTAGAAGTTT-
          1 AGGGTCAAAAATGGGATTTTTAGAAGTTTG

                 *  **   *       *         
      12311 AGGGTTAATTATGAGATTTTTGGAAGTTTTG
          1 AGGGTCAAAAATGGGATTTTTAGAAG-TTTG

                 *               *     *  
      12342 -GGGTTAAAAATGGGATTTTTGGAAGTCTG
          1 AGGGTCAAAAATGGGATTTTTAGAAGTTTG

                          *      
      12371 AGGGT-AAAAATGGAATTTTT
          1 AGGGTCAAAAATGGGATTTTT

      12391 GAACAATTTA


Statistics
Matches: 215,  Mismatches: 29, Indels: 27
        0.79            0.11        0.10

Matches are distributed among these distances:
  28    1  0.00
  29   99  0.46
  30  100  0.47
  31   15  0.07

ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38


Consensus pattern (30 bp):   
AGGGTCAAAAATGGGATTTTTAGAAGTTTG

Found at i:12173 original size:59 final size:58

Alignment explanation


    Indices: 12105--12391  Score: 362
    Period size: 59  Copynumber: 4.8  Consensus size: 58

      12095 GGAAAATTCA

                                                             *         
      12105 GGGTCAAAAATGGGATTTTTAGAAGTTTGAGGGTAAAAATGGTATTTTTTGAAGTTTTG
          1 GGGTCAAAAATGGGATTTTTAGAAGTTTGAGGGTAAAAATGG-ATTTTTGGAAGTTTTG

                *       *                                             * 
      12164 GGGTTAAAAATGAGATTTTTTAGAAGTTTGAGGGTAAAAATGGGATTTTTGGAAGTTTCG
          1 GGGTCAAAAATGGGA-TTTTTAGAAGTTTGAGGGTAAAAAT-GGATTTTTGGAAGTTTTG

            *                           * *                      *      
      12224 AGGTCAAAAATGGGATTTTTAGAAG-TTCAAGGTCAAAAATAGGATTTTTGGATGTTTTG
          1 GGGTCAAAAATGGGATTTTTAGAAGTTTGAGGGT-AAAAAT-GGATTTTTGGAAGTTTTG

                     *                           **                     
      12283 GGGTCAAAATTGGGATTTTTAGAAGTTT-AGGGTTAATTATGAGATTTTTGGAAGTTTTG
          1 GGGTCAAAAATGGGATTTTTAGAAGTTTGAGGG-TAAAAATG-GATTTTTGGAAGTTTTG

                *               *     *                       
      12342 GGGTTAAAAATGGGATTTTTGGAAGTCTGAGGGTAAAAATGGAATTTTTG
          1 GGGTCAAAAATGGGATTTTTAGAAGTTTGAGGGTAAAAATGG-ATTTTTG

      12392 AACAATTTAG


Statistics
Matches: 196,  Mismatches: 24, Indels: 16
        0.83            0.10        0.07

Matches are distributed among these distances:
  58    8  0.04
  59  128  0.65
  60   58  0.30
  61    2  0.01

ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38


Consensus pattern (58 bp):   
GGGTCAAAAATGGGATTTTTAGAAGTTTGAGGGTAAAAATGGATTTTTGGAAGTTTTG

Done.