Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007330.1 Kokia drynarioides strain JFW-HI SEQ_121946, 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: 13075
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37


Found at i:1827 original size:27 final size:27

Alignment explanation


    Indices: 1774--1831  Score: 66
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       1764 AAGTTTTAAG

                        *      *  *    
       1774 ATATTTTTTTAATTCTAAATTTGAAAT
          1 ATATTTTTTTAAATCTAAAATTAAAAT

                                        
       1801 ATATATTTTTTAAAT-TAAAATTAAAAT
          1 ATAT-TTTTTTAAATCTAAAATTAAAAT

                 
       1828 -TATT
          1 ATATT

       1832 AAAAATATTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  25    1  0.04
  26    3  0.11
  27   14  0.52
  28    9  0.33

ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53


Consensus pattern (27 bp):   
ATATTTTTTTAAATCTAAAATTAAAAT

Found at i:1977 original size:27 final size:27

Alignment explanation


    Indices: 1947--2003  Score: 62
    Period size: 28  Copynumber: 2.1  Consensus size: 27

       1937 TTATTTTTTT

                            *  *        
       1947 AATA-TAATTTTTTAATTTTAAATTCAA
          1 AATACTAATTTTTTAAATTGAAATT-AA

                  **                   
       1974 AATACTTTTTTTTTAAATTGAAATTAA
          1 AATACTAATTTTTTAAATTGAAATTAA

               
       2001 AAT
          1 AAT

       2004 TAAATATATT


Statistics
Matches: 25,  Mismatches: 4, Indels: 2
        0.81            0.13        0.06

Matches are distributed among these distances:
  27    9  0.36
  28   16  0.64

ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51


Consensus pattern (27 bp):   
AATACTAATTTTTTAAATTGAAATTAA

Found at i:2177 original size:115 final size:111

Alignment explanation


    Indices: 1954--2179  Score: 267
    Period size: 115  Copynumber: 2.0  Consensus size: 111

       1944 TTTAATATAA

                                             *   * *   *     *               
       1954 TTTTTTAATTTTAAATTCAAAATACTTTTTTTTTAAATTGAAATTAAAATTAAATATATTAAAAG
          1 TTTTTTAATTTTAAATTCAAAATACTTTTTTTTAAAACTAAAACTAAAAATAAATATATTAAAAG

                          *                     * *        
       2019 TATTTAAACGATAAGTAAAGAGTTGATGTTTTAAAATGTAAATTTAT
         66 TATTTAAACGATAAATAAAGAGTTGA-GTTTTAAAAAGAAAATTTAT

                                                                            *
       2066 TTTTTTAATTTTAAA-TCAAAAATACATATTTTTTTAAAAACTAAAACTAAAAATAAATATATTG
          1 TTTTTTAATTTTAAATTC-AAAATAC-T-TTTTTTT-AAAACTAAAACTAAAAATAAATATATTA

            *           * *                                    
       2130 GAAGTATTTAAAGGTTAAATAAAGAGTT-AGATTTTAAAACAGAAAATTTA
         62 AAAGTATTTAAACGATAAATAAAGAGTTGAG-TTTTAAAA-AGAAAATTTA

       2180 CTGTATAATT


Statistics
Matches: 96,  Mismatches: 12, Indels: 9
        0.82            0.10        0.08

Matches are distributed among these distances:
 111    2  0.02
 112   22  0.23
 113    2  0.02
 114   16  0.17
 115   54  0.56

ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42


Consensus pattern (111 bp):   
TTTTTTAATTTTAAATTCAAAATACTTTTTTTTAAAACTAAAACTAAAAATAAATATATTAAAAG
TATTTAAACGATAAATAAAGAGTTGAGTTTTAAAAAGAAAATTTAT

Found at i:2753 original size:26 final size:29

Alignment explanation


    Indices: 2724--2777  Score: 78
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       2714 ATTAAAATAA

                                         
       2724 ATTTAAA-TTT-CA-AATAATTAGAAAAT
          1 ATTTAAATTTTACATAATAATTAGAAAAT

                        *               
       2750 ATTTAAATTTTAGATAATAATTAGAAAA
          1 ATTTAAATTTTACATAATAATTAGAAAA

       2778 CTCGCAAGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  26    7  0.29
  27    3  0.12
  28    1  0.04
  29   13  0.54

ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39


Consensus pattern (29 bp):   
ATTTAAATTTTACATAATAATTAGAAAAT
Done.