Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005819.1 Kokia drynarioides strain JFW-HI SEQ_120103, 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, 923

Length: 1539
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Found at i:562 original size:43 final size:43

Alignment explanation


    Indices: 483--564  Score: 112
    Period size: 43  Copynumber: 1.9  Consensus size: 43

        473 AACATGTTAA

                               *        *              
        483 ATTATATTACTTGACTCGTGTTAATATAGTTGCATGTTACTAG
          1 ATTATATTACTTGACTCGTATTAATATACTTGCATGTTACTAG

                        *    *                      
        526 ATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
          1 ATTATATTACTTGACTCGTATTAATATACTTG-CATGTTA

        565 TTAATTGTGC


Statistics
Matches: 34,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  42    3  0.09
  43   31  0.91

ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48


Consensus pattern (43 bp):   
ATTATATTACTTGACTCGTATTAATATACTTGCATGTTACTAG

Found at i:1181 original size:45 final size:45

Alignment explanation


    Indices: 1114--1250  Score: 193
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       1104 GCATAGCTCA

                                                  **     
       1114 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC

                             *     *             *       
       1159 TCAAGCCAAGGATATCAACCTCAATTTGACGAGCCACTACAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC

                 **           *  *                       
       1204 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCACCACAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC

              
       1249 TC
          1 TC

       1251 TATTCCTCCC


Statistics
Matches: 80,  Mismatches: 12, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  45   80  1.00

ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC

Found at i:1269 original size:21 final size:21

Alignment explanation


    Indices: 1243--1287  Score: 72
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1233 CGAGCCACCA

                      *          
       1243 CAATACTCTATTCCTCCCGGG
          1 CAATACTCTACTCCTCCCGGG

                             *   
       1264 CAATACTCTACTCCTCCGGGG
          1 CAATACTCTACTCCTCCCGGG

               
       1285 CAA
          1 CAA

       1288 ATGGACCTTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24


Consensus pattern (21 bp):   
CAATACTCTACTCCTCCCGGG
Done.