Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013999.1 Kokia drynarioides strain JFW-HI SEQ_129030, 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: 7119
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30


Found at i:978 original size:39 final size:39

Alignment explanation


    Indices: 930--1047  Score: 148
    Period size: 39  Copynumber: 3.1  Consensus size: 39

        920 TCATTACCTA

                *     *    *            *          
        930 GCTTCACGGTGTTTATAGTGTCACCGTCGGTTCAGTATT
          1 GCTTTACGGTATTTACAGTGTCACCGTCAGTTCAGTATT

                                 *                 
        969 GCTTTACGGTATTTACAGTGTTACCGTCAGTTCAGTATT
          1 GCTTTACGGTATTTACAGTGTCACCGTCAGTTCAGTATT

              *                  *  *    *         
       1008 GCATTACGGTATTTACAGTGTTACTGTCAATTCAGT-TT
          1 GCTTTACGGTATTTACAGTGTCACCGTCAGTTCAGTATT

              
       1046 GC
          1 GC

       1048 ATTGCAGCGT


Statistics
Matches: 71,  Mismatches: 8, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  38    4  0.06
  39   67  0.94

ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40


Consensus pattern (39 bp):   
GCTTTACGGTATTTACAGTGTCACCGTCAGTTCAGTATT

Found at i:1026 original size:22 final size:21

Alignment explanation


    Indices: 962--1026  Score: 50
    Period size: 22  Copynumber: 3.2  Consensus size: 21

        952 ACCGTCGGTT

                                  
        962 CAGTATTGCTTTACGGTATTTA
          1 CAGTATTGC-TTACGGTATTTA

                         *    *   
        984 CAG---TG-TTACCGTCAGTT-
          1 CAGTATTGCTTACGGT-ATTTA

                                  
       1001 CAGTATTGCATTACGGTATTTA
          1 CAGTATTGC-TTACGGTATTTA

                
       1023 CAGT
          1 CAGT

       1027 GTTACTGTCA


Statistics
Matches: 32,  Mismatches: 4, Indels: 14
        0.64            0.08        0.28

Matches are distributed among these distances:
  17    9  0.28
  18    3  0.09
  19    2  0.06
  20    2  0.06
  21    3  0.09
  22   13  0.41

ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40


Consensus pattern (21 bp):   
CAGTATTGCTTACGGTATTTA

Found at i:1061 original size:38 final size:39

Alignment explanation


    Indices: 941--1082  Score: 133
    Period size: 39  Copynumber: 3.7  Consensus size: 39

        931 CTTCACGGTG

                *     *  *   *            *    * * 
        941 TTTATAGTGTCACCGTCGGTTCAGTATTGCTTTACGGTA
          1 TTTACAGTGTTACTGTCAGTTCAGTATTGCATTACAGCA

                         *                     * * 
        980 TTTACAGTGTTACCGTCAGTTCAGTATTGCATTACGGTA
          1 TTTACAGTGTTACTGTCAGTTCAGTATTGCATTACAGCA

                              *              *    *
       1019 TTTACAGTGTTACTGTCAATTCAGT-TTGCATTGCAGCG
          1 TTTACAGTGTTACTGTCAGTTCAGTATTGCATTACAGCA

                  *   *    *          
       1057 TTTACATTGTCACTGCCAGTTCAGTA
          1 TTTACAGTGTTACTGTCAGTTCAGTA

       1083 GTTTGATAAC


Statistics
Matches: 88,  Mismatches: 14, Indels: 2
        0.85            0.13        0.02

Matches are distributed among these distances:
  38   30  0.34
  39   58  0.66

ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39


Consensus pattern (39 bp):   
TTTACAGTGTTACTGTCAGTTCAGTATTGCATTACAGCA
Done.