Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002226.1 Kokia drynarioides strain JFW-HI SEQ_114224, 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: 13257
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38


Found at i:2834 original size:29 final size:30

Alignment explanation


    Indices: 2791--2849  Score: 84
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       2781 AAATTGGATC

                     *               *    
       2791 AAATCAAAATTTCATGTATAAAATTGCACA
          1 AAATCAAAAGTTCATGTATAAAATTACACA

                                *         
       2821 AAATC-AAAGTTCATGTATACAATTACACA
          1 AAATCAAAAGTTCATGTATAAAATTACACA

       2850 TTAAACCGTA


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  29   21  0.81
  30    5  0.19

ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29


Consensus pattern (30 bp):   
AAATCAAAAGTTCATGTATAAAATTACACA

Found at i:7305 original size:3 final size:3

Alignment explanation


    Indices: 7297--7333  Score: 74
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       7287 ATTCAGTCCG

                                                             
       7297 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T

       7334 TTAAATGTCC


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:9831 original size:91 final size:87

Alignment explanation


    Indices: 9669--9851  Score: 237
    Period size: 91  Copynumber: 2.1  Consensus size: 87

       9659 GCCTTTTTTG

                                                                         *   
       9669 TTTTTAGTTTAAAAGTAATAGTTCTGTTCTTGAATTAAATCGTATTATTTTTGTGTAATTTTTTA
          1 TTTTTAGTTTAAAAGTAATAGTTCTGTTCTTGAATTAAATCGTATTATTTTTGTGTAATTTCTTA

                                  
       9734 GCAATCCGACTGGAT-CGT-CT
         66 GCAATCCGACTGGATCCGTACT

                       *   *                     *                           
       9754 TTTTTAAGTTTTAAATTAATAGTT-TGTTCTTGAATTGAATCGTATTTCTGGTATTTTTGTGTAA
          1 TTTTT-AGTTTAAAAGTAATAGTTCTGTTCTTGAATTAAATCGTA----T--TATTTTTGTGTAA

                    *                    
       9818 TTTCTTAGTAATCCGACTGGATCCGTACT
         59 TTTCTTAGCAATCCGACTGGATCCGTACT

                 
       9847 TTTTT
          1 TTTTT

       9852 TTCTGTTGAT


Statistics
Matches: 84,  Mismatches: 5, Indels: 10
        0.85            0.05        0.10

Matches are distributed among these distances:
  85   24  0.29
  86   16  0.19
  89    1  0.01
  91   33  0.39
  92    3  0.04
  93    7  0.08

ACGTcount: A:0.24, C:0.10, G:0.15, T:0.50


Consensus pattern (87 bp):   
TTTTTAGTTTAAAAGTAATAGTTCTGTTCTTGAATTAAATCGTATTATTTTTGTGTAATTTCTTA
GCAATCCGACTGGATCCGTACT

Found at i:9892 original size:108 final size:108

Alignment explanation


    Indices: 9753--9948  Score: 311
    Period size: 108  Copynumber: 1.8  Consensus size: 108

       9743 CTGGATCGTC

                                   *  *                      * *   *         
       9753 TTTTTTAAGTTTTAAATTAATAGTTTGTTCTTGAATTGAATCGTATTTCTGGTATTTTTGTGTAA
          1 TTTTTTAAGTTTTAAATTAATAGGTTATTCTTGAATTGAATCGTATTTCAGATATATTTGTGTAA

                    *                                  
       9818 TTTCTTAGTAATCCGACTGGATCCGTACTTTTTTTTCTGTTGA
         66 TTTCTTAGCAATCCGACTGGATCCGTACTTTTTTTTCTGTTGA

                               *                 *                         * 
       9861 TTTTTTAAGTTTTAAATTAGTAGGTTATTCTTGAATTTAATCGTATTTCAGATATATTTGTGTGA
          1 TTTTTTAAGTTTTAAATTAATAGGTTATTCTTGAATTGAATCGTATTTCAGATATATTTGTGTAA

                                   
       9926 TTTCTTAGCAATCCGACTGGATC
         66 TTTCTTAGCAATCCGACTGGATC

       9949 GTCATTGAAC


Statistics
Matches: 79,  Mismatches: 9, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
 108   79  1.00

ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51


Consensus pattern (108 bp):   
TTTTTTAAGTTTTAAATTAATAGGTTATTCTTGAATTGAATCGTATTTCAGATATATTTGTGTAA
TTTCTTAGCAATCCGACTGGATCCGTACTTTTTTTTCTGTTGA
Done.