Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010294.1 Kokia drynarioides strain JFW-HI SEQ_125146, 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: 4816
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:111 original size:35 final size:36

Alignment explanation


    Indices: 60--137  Score: 106
    Period size: 35  Copynumber: 2.2  Consensus size: 36

         50 TTTGTTATGG

                                                  
         60 ATGCGAATGAAAATGGACCTCACAACT-GGTTTC-CAA
          1 ATGC-AATGAAAATGGACCTCACAA-TAGGTTTCTCAA

                               *             *  
         96 ATGCAATGAAAATGGACCTTACAATAGGTTTCTTAA
          1 ATGCAATGAAAATGGACCTCACAATAGGTTTCTCAA

                  
        132 ATGCAA
          1 ATGCAA

        138 ATGAGAGAGA


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  34    1  0.03
  35   25  0.66
  36   12  0.32

ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26


Consensus pattern (36 bp):   
ATGCAATGAAAATGGACCTCACAATAGGTTTCTCAA

Found at i:3303 original size:59 final size:58

Alignment explanation


    Indices: 3135--3410  Score: 306
    Period size: 58  Copynumber: 4.7  Consensus size: 58

       3125 GTAAAACGAT

                       *   *                        *  * *          * 
       3135 AATTTTGGACACTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGTGGTCAAAAATAG
          1 AATTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG

             *    *                                      *             
       3193 -TTTTTAGACATTCGAGGGGTAAAATGGTAATTTTTGGAAG-TTTCGGGTCAAAAATGG
          1 AATTTTGGACATTCG-GGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG

                          *           *         *                      
       3250 AATTTTTGGACATTAGGGGGTAAAATAGTAATTTTTAGAAGTTTTGGGGTCAAAAATGG
          1 AA-TTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG

                *    *   *             *         *       *         *  *
       3309 AATTCTGGATATTTGGGGGTAAAAATGATAATTTTTGAAAGTTTTAGGGTCAAAATTGT
          1 AATTTTGGACATTCGGGGGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG

                          *                             
       3368 AATTTTGGACA-TCCGGGGTAAAATGGTAATTTTTGGAAAGTTT
          1 AATTTTGGACATTCGGGGGTAAAATGGTAATTTTTGG-AAGTTT

       3411 AAGGTAAAAA


Statistics
Matches: 182,  Mismatches: 30, Indels: 12
        0.81            0.13        0.05

Matches are distributed among these distances:
  57   39  0.21
  58   74  0.41
  59   69  0.38

ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36


Consensus pattern (58 bp):   
AATTTTGGACATTCGGGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG

Found at i:3452 original size:30 final size:30

Alignment explanation


    Indices: 3325--3457  Score: 87
    Period size: 30  Copynumber: 4.4  Consensus size: 30

       3315 GGATATTTGG

                               *       ** 
       3325 GGGTAAAAATGATAATTTTTGAAAGTTTTA
          1 GGGTAAAAATGATAATTTTGGAAAGTTCGA

                     *             *   *   
       3355 GGGTCAAAATTG-TAATTTTGGACA-TCCG-
          1 GGGT-AAAAATGATAATTTTGGAAAGTTCGA

                       *                 * 
       3383 GGGT-AAAATGGTAATTTTTGGAAAGTT-TA
          1 GGGTAAAAATGATAA-TTTTGGAAAGTTCGA

            *              *    *          
       3412 AGGTAAAAAATGATATTTTTTGAAAGTTCGA
          1 GGGT-AAAAATGATAATTTTGGAAAGTTCGA

                           
       3443 GGGTCAAAATATGAT
          1 GGGT-AAAA-ATGAT

       3458 TTCTAGACAT


Statistics
Matches: 77,  Mismatches: 17, Indels: 16
        0.70            0.15        0.15

Matches are distributed among these distances:
  26    5  0.06
  27    3  0.04
  28   12  0.16
  29    5  0.06
  30   25  0.32
  31   22  0.29
  32    5  0.06

ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35


Consensus pattern (30 bp):   
GGGTAAAAATGATAATTTTGGAAAGTTCGA
Done.