Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002168.1 Kokia drynarioides strain JFW-HI SEQ_114125, 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: 20671
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:7574 original size:17 final size:17

Alignment explanation


    Indices: 7552--7590  Score: 69
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       7542 AGGTGAAGAA

                     *       
       7552 CTTGTTCGTTGAGAATT
          1 CTTGTTCGTAGAGAATT

                             
       7569 CTTGTTCGTAGAGAATT
          1 CTTGTTCGTAGAGAATT

                 
       7586 CTTGT
          1 CTTGT

       7591 CAATGTGGAG


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46


Consensus pattern (17 bp):   
CTTGTTCGTAGAGAATT

Found at i:14937 original size:24 final size:24

Alignment explanation


    Indices: 14881--14955  Score: 91
    Period size: 24  Copynumber: 3.2  Consensus size: 24

      14871 AATAACAACC

                  *                  
      14881 AAAACAACAACAAAAATAATAGA-A
          1 AAAACAGCAACAAAAATAATA-ATA

                *                   
      14905 AAAATAGCAACAAAAATAATAATA
          1 AAAACAGCAACAAAAATAATAATA

             *       *              
      14929 ATAACAGCATC-AAAATAATAATA
          1 AAAACAGCAACAAAAATAATAATA

                
      14952 AAAA
          1 AAAA

      14956 GCCCCAAAAC


Statistics
Matches: 44,  Mismatches: 6, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  23   16  0.36
  24   28  0.64

ACGTcount: A:0.71, C:0.11, G:0.04, T:0.15


Consensus pattern (24 bp):   
AAAACAGCAACAAAAATAATAATA

Found at i:15025 original size:22 final size:21

Alignment explanation


    Indices: 14986--15075  Score: 81
    Period size: 22  Copynumber: 4.1  Consensus size: 21

      14976 ATAGTAATTA

                  *      *       *
      14986 AAAAAAAAAGCACTAAAACAAT
          1 AAAAAACAA-CACCAAAACAAC

                                * 
      15008 AAAAACACAACACCAAAACAGC
          1 AAAAA-ACAACACCAAAACAAC

                  * *           * 
      15030 AAAAAATAGCAACCAAAACAGC
          1 AAAAAACAAC-ACCAAAACAAC

                                  
      15052 AAAAAAACAACACCAAAACAAC
          1 -AAAAAACAACACCAAAACAAC

              
      15074 AA
          1 AA

      15076 TATATTTTTT


Statistics
Matches: 56,  Mismatches: 9, Indels: 7
        0.78            0.12        0.10

Matches are distributed among these distances:
  21    5  0.09
  22   40  0.71
  23   11  0.20

ACGTcount: A:0.69, C:0.23, G:0.04, T:0.03


Consensus pattern (21 bp):   
AAAAAACAACACCAAAACAAC

Found at i:15035 original size:44 final size:44

Alignment explanation


    Indices: 14987--15071  Score: 118
    Period size: 44  Copynumber: 2.0  Consensus size: 44

      14977 TAGTAATTAA

                         *       *     *                
      14987 AAAAAAAAGC-ACTAAAACAATAAAAACACAACACCAAAACAGC
          1 AAAAAAAAGCAACCAAAACAACAAAAAAACAACACCAAAACAGC

                  *             *                     
      15030 AAAAAATAGCAACCAAAACAGCAAAAAAACAACACCAAAACA
          1 AAAAAAAAGCAACCAAAACAACAAAAAAACAACACCAAAACA

      15072 ACAATATATT


Statistics
Matches: 36,  Mismatches: 5, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  43    9  0.25
  44   27  0.75

ACGTcount: A:0.68, C:0.24, G:0.05, T:0.04


Consensus pattern (44 bp):   
AAAAAAAAGCAACCAAAACAACAAAAAAACAACACCAAAACAGC

Found at i:18975 original size:35 final size:35

Alignment explanation


    Indices: 18924--18991  Score: 109
    Period size: 35  Copynumber: 1.9  Consensus size: 35

      18914 AAGTATTTTG

                *                   *          
      18924 ATAATTAGTATAATAACACATTTAGTCTCTAATTT
          1 ATAACTAGTATAATAACACATTTAATCTCTAATTT

                                        *    
      18959 ATAACTAGTATAATAACACATTTAATCTTTAAT
          1 ATAACTAGTATAATAACACATTTAATCTCTAAT

      18992 ACTTACATAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  35   30  1.00

ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41


Consensus pattern (35 bp):   
ATAACTAGTATAATAACACATTTAATCTCTAATTT

Found at i:19886 original size:31 final size:30

Alignment explanation


    Indices: 19829--19886  Score: 71
    Period size: 31  Copynumber: 1.9  Consensus size: 30

      19819 TTTGATTAAA

                *      *                  
      19829 AAATTTGAAGATCAAATTGATAGAATTTAT
          1 AAATATGAAGAGCAAATTGATAGAATTTAT

                               *  *     
      19859 AAATATGAAGAGCTAAATTTATTGAATT
          1 AAATATGAAGAGC-AAATTGATAGAATT

      19887 ATTTAAAATT


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  30   11  0.48
  31   12  0.52

ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36


Consensus pattern (30 bp):   
AAATATGAAGAGCAAATTGATAGAATTTAT

Found at i:19957 original size:21 final size:18

Alignment explanation


    Indices: 19911--19946  Score: 56
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      19901 TTAAATTGAT

                              
      19911 AAAA-TAAATATATATTA
          1 AAAATTAAATATATATTA

                               
      19928 AAAATTAAATATATTATTA
          1 AAAATTAAATATA-TATTA

      19947 TACCAATTAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    4  0.24
  18    8  0.47
  19    5  0.29

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (18 bp):   
AAAATTAAATATATATTA
Done.