Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013502.1 Kokia drynarioides strain JFW-HI SEQ_128528, 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: 26529
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33


Found at i:20871 original size:23 final size:23

Alignment explanation


    Indices: 20811--20931  Score: 111
    Period size: 23  Copynumber: 5.2  Consensus size: 23

      20801 ACACTAGCGC

                                   
      20811 GCTCTCTGTTTAGCACTGTGTGT
          1 GCTCTCTGTTTAGCACTGTGTGT

             * *   *  *            
      20834 GTTTTCTATTCAGCACTGTGTGT
          1 GCTCTCTGTTTAGCACTGTGTGT

                               *    
      20857 GCTCTCTGTTTAGCAC-GTCTCGT
          1 GCTCTCTGTTTAGCACTGTGT-GT

                                  **  
      20880 GCTCTCTGTTATTAGCACT-TCACGT
          1 GCTCTCTG-T-TTAGCACTGT-GTGT

                    *        *     
      20905 GCTCTCTGATTAGCACTTTGTGT
          1 GCTCTCTGTTTAGCACTGTGTGT

                
      20928 GCTC
          1 GCTC

      20932 AGTACTTTGT


Statistics
Matches: 78,  Mismatches: 14, Indels: 12
        0.75            0.13        0.12

Matches are distributed among these distances:
  22    3  0.04
  23   55  0.71
  24    2  0.03
  25   18  0.23

ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42


Consensus pattern (23 bp):   
GCTCTCTGTTTAGCACTGTGTGT

Found at i:20894 original size:25 final size:24

Alignment explanation


    Indices: 20855--20920  Score: 91
    Period size: 25  Copynumber: 2.8  Consensus size: 24

      20845 AGCACTGTGT

                                  * 
      20855 GTGCTCTCTGT-TTAGCACGTCTC
          1 GTGCTCTCTGTATTAGCACGTCAC

                                *    
      20878 GTGCTCTCTGTTATTAGCACTTCAC
          1 GTGCTCTCTG-TATTAGCACGTCAC

                               
      20903 GTGCTCTCTG-ATTAGCAC
          1 GTGCTCTCTGTATTAGCAC

      20921 TTTGTGTGCT


Statistics
Matches: 39,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  23   18  0.46
  24    1  0.03
  25   20  0.51

ACGTcount: A:0.14, C:0.29, G:0.20, T:0.38


Consensus pattern (24 bp):   
GTGCTCTCTGTATTAGCACGTCAC

Found at i:20962 original size:23 final size:23

Alignment explanation


    Indices: 20932--20994  Score: 117
    Period size: 23  Copynumber: 2.7  Consensus size: 23

      20922 TTGTGTGCTC

                        *          
      20932 AGTACTTTGTGTACTCTTTATTT
          1 AGTACTTTGTGTGCTCTTTATTT

                                   
      20955 AGTACTTTGTGTGCTCTTTATTT
          1 AGTACTTTGTGTGCTCTTTATTT

                             
      20978 AGTACTTTGTGTGCTCT
          1 AGTACTTTGTGTGCTCT

      20995 CTGTTGTCTA


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  23   39  1.00

ACGTcount: A:0.14, C:0.14, G:0.17, T:0.54


Consensus pattern (23 bp):   
AGTACTTTGTGTGCTCTTTATTT

Found at i:24730 original size:17 final size:18

Alignment explanation


    Indices: 24708--24743  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      24698 TAAATGAGTT

                              
      24708 AATTAGGAT-TAAATTGG
          1 AATTAGGATATAAATTGG

                   *          
      24725 AATTAGGGTATAAATTGG
          1 AATTAGGATATAAATTGG

             
      24743 A
          1 A

      24744 TAGAAATTCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    8  0.47
  18    9  0.53

ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33


Consensus pattern (18 bp):   
AATTAGGATATAAATTGG

Found at i:25062 original size:18 final size:18

Alignment explanation


    Indices: 25039--25075  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      25029 TTTGTGATCA

                              
      25039 AAATTGAAAATGAAAGTG
          1 AAATTGAAAATGAAAGTG

                  *  *        
      25057 AAATTGGAATTGAAAGTG
          1 AAATTGAAAATGAAAGTG

             
      25075 A
          1 A

      25076 TATGAATTGT


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

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24


Consensus pattern (18 bp):   
AAATTGAAAATGAAAGTG
Done.