Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007440.1 Kokia drynarioides strain JFW-HI SEQ_122061, 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: 3078
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:2063 original size:60 final size:58

Alignment explanation


    Indices: 1999--2169  Score: 207
    Period size: 59  Copynumber: 2.9  Consensus size: 58

       1989 AATTGAATCT

                   *   *   *                           *     * *       *
       1999 AAAAAAACTTAAGTATCAAATTAGGAAAAAAATATCAAGTTCAGGTATCGATTTGAGTCC
          1 AAAAAAATTTAGGTACCAAATTAGG-AAAAAATATCAAGTTCATGTATCAAATTGAGT-A

                                   *        *    *        *       *   
       2059 AAAAAAATTTAGGTACCAAATTAAGAAAAAATGTCAATTTCATGTACCAAATTGGGTA
          1 AAAAAAATTTAGGTACCAAATTAGGAAAAAATATCAAGTTCATGTATCAAATTGAGTA

                                                                 
       2117 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATATCAAGTTCATGTATCAAAT
          1 AAAAAAA-TTTAGGTACCAAATTAGGAAAAAATATCAAGTTCATGTATCAAAT

       2170 GTTATATTAA


Statistics
Matches: 94,  Mismatches: 16, Indels: 3
        0.83            0.14        0.03

Matches are distributed among these distances:
  58    7  0.07
  59   66  0.70
  60   21  0.22

ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27


Consensus pattern (58 bp):   
AAAAAAATTTAGGTACCAAATTAGGAAAAAATATCAAGTTCATGTATCAAATTGAGTA

Found at i:2106 original size:31 final size:30

Alignment explanation


    Indices: 2071--2169  Score: 89
    Period size: 31  Copynumber: 3.3  Consensus size: 30

       2061 AAAAATTTAG

                       *                   
       2071 GTACCAAATTAAGAAAAAATGTCAATTTCAT
          1 GTACCAAATTAGGAAAAAAT-TCAATTTCAT

                      *                    *
       2102 GTACCAAATTGGGTAAAAAA---AAGTTT-AG
          1 GTACCAAATTAGG-AAAAAATTCAA-TTTCAT

                                     *     
       2130 GTACCAAATTAGGAAAAAATATCAAGTTCAT
          1 GTACCAAATTAGGAAAAAAT-TCAATTTCAT

               *     
       2161 GTATCAAAT
          1 GTACCAAAT

       2170 GTTATATTAA


Statistics
Matches: 54,  Mismatches: 7, Indels: 14
        0.72            0.09        0.19

Matches are distributed among these distances:
  27    6  0.11
  28   15  0.28
  29    3  0.06
  30    2  0.04
  31   22  0.41
  32    6  0.11

ACGTcount: A:0.47, C:0.11, G:0.14, T:0.27


Consensus pattern (30 bp):   
GTACCAAATTAGGAAAAAATTCAATTTCAT

Found at i:2147 original size:28 final size:27

Alignment explanation


    Indices: 2059--2148  Score: 90
    Period size: 28  Copynumber: 3.1  Consensus size: 27

       2049 ATTTGAGTCC

                                   *   
       2059 AAAAAAATTTAGGTACCAAATTAAGAA
          1 AAAAAAATTTAGGTACCAAATTAGGAA

                   *       *          *     
       2086 AAAATGTCAATTTCATGTACCAAATTGGGTAA
          1 AAAA---AAATTT-AGGTACCAAATTAGG-AA

                  *                    
       2118 AAAAAAGTTTAGGTACCAAATTAGGAA
          1 AAAAAAATTTAGGTACCAAATTAGGAA

                
       2145 AAAA
          1 AAAA

       2149 TATCAAGTTC


Statistics
Matches: 50,  Mismatches: 8, Indels: 10
        0.74            0.12        0.15

Matches are distributed among these distances:
  27   10  0.20
  28   13  0.26
  29    4  0.08
  30    5  0.10
  31   12  0.24
  32    6  0.12

ACGTcount: A:0.52, C:0.09, G:0.14, T:0.24


Consensus pattern (27 bp):   
AAAAAAATTTAGGTACCAAATTAGGAA
Done.