Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001249.1 Kokia drynarioides strain JFW-HI SEQ_112620, 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: 1996
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34


Found at i:253 original size:11 final size:10

Alignment explanation


    Indices: 228--252  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

        218 TATGGGAGAC

                      
        228 AAAAACAAAA
          1 AAAAACAAAA

                      
        238 AAAAACAAAA
          1 AAAAACAAAA

                 
        248 AAAAA
          1 AAAAA

        253 AGAAGGGTGC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00


Consensus pattern (10 bp):   
AAAAACAAAA

Found at i:560 original size:21 final size:20

Alignment explanation


    Indices: 536--579  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 20

        526 TTTCTTCATT

                                  
        536 ATTTT-TTTTCTTTTAAATCTA
          1 ATTTTATTTT-TTTTAAAT-TA

                                 
        557 ATTTTAATTTTTTTTAAATTA
          1 ATTTT-ATTTTTTTTAAATTA

              
        578 AT
          1 AT

        580 CAGACTAAAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  21    9  0.43
  22    8  0.38
  23    4  0.19

ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66


Consensus pattern (20 bp):   
ATTTTATTTTTTTTAAATTA

Found at i:968 original size:19 final size:19

Alignment explanation


    Indices: 946--984  Score: 60
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        936 TTTAATTTTT

                      *        
        946 AAAAAATTTATTAAATAAA
          1 AAAAAATTTAATAAATAAA

                *              
        965 AAAATATTTAATAAATAAA
          1 AAAAAATTTAATAAATAAA

             
        984 A
          1 A

        985 TTAAATTATA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (19 bp):   
AAAAAATTTAATAAATAAA

Found at i:1800 original size:52 final size:52

Alignment explanation


    Indices: 1720--1818  Score: 162
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       1710 ATTCTCTGAC

                            *      *                            
       1720 CTTTAGCGGCGCTTATTGGAAAGTGCCGCTAATGACCTGACATTTAGTGGCA
          1 CTTTAGCGGCGCTTATAGGAAAGCGCCGCTAATGACCTGACATTTAGTGGCA

                       *                             *     
       1772 CTTTAGCGGCGGTTATAGGAAAGCGCCGCTAATGACCTGACCTTTAG
          1 CTTTAGCGGCGCTTATAGGAAAGCGCCGCTAATGACCTGACATTTAG

       1819 CAGCACTTGA


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  52   43  1.00

ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27


Consensus pattern (52 bp):   
CTTTAGCGGCGCTTATAGGAAAGCGCCGCTAATGACCTGACATTTAGTGGCA

Found at i:1834 original size:41 final size:40

Alignment explanation


    Indices: 1789--1994  Score: 295
    Period size: 41  Copynumber: 5.0  Consensus size: 40

       1779 GGCGGTTATA

                                                     
       1789 GGAAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTTGAG
          1 GGAAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTT-AG

                                           *  *     
       1830 GGAAAGCGCCGCTAATGACCTGACCTTTAGCGGCTCTTAG
          1 GGAAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTTAG

              *      *                                
       1870 GTAAAAGCGTCGCTAATGACCTGACCTTTAGCAGCACTTAAG
          1 G-GAAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTT-AG

                    *                         *     
       1912 GGAAAGCGTCGCTAATGACCTGACCTTTAGCAGCTCTTAG
          1 GGAAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTTAG

              *                             *  *     
       1952 GTAAAAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTTAG
          1 G-GAAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTTAG

              
       1993 GG
          1 GG

       1995 GA


Statistics
Matches: 149,  Mismatches: 13, Indels: 7
        0.88            0.08        0.04

Matches are distributed among these distances:
  40    6  0.04
  41  140  0.94
  42    3  0.02

ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22


Consensus pattern (40 bp):   
GGAAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTTAG

Found at i:1914 original size:82 final size:82

Alignment explanation


    Indices: 1791--1983  Score: 350
    Period size: 82  Copynumber: 2.4  Consensus size: 82

       1781 CGGTTATAGG

                                                *                            
       1791 AAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTTGAGGGAAAGCGCCGCTAATGACCTGACCT
          1 AAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTTAAGGGAAAGCGCCGCTAATGACCTGACCT

                 *           
       1856 TTAGCGGCTCTTAGGTA
         66 TTAGCAGCTCTTAGGTA

                  *                                        *                 
       1873 AAAGCGTCGCTAATGACCTGACCTTTAGCAGCACTTAAGGGAAAGCGTCGCTAATGACCTGACCT
          1 AAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTTAAGGGAAAGCGCCGCTAATGACCTGACCT

                             
       1938 TTAGCAGCTCTTAGGTA
         66 TTAGCAGCTCTTAGGTA

                                         
       1955 AAAGCGCCGCTAATGACCTGACCTTTAGC
          1 AAAGCGCCGCTAATGACCTGACCTTTAGC

       1984 GGCGCTTAGG


Statistics
Matches: 106,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  82  106  1.00

ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23


Consensus pattern (82 bp):   
AAAGCGCCGCTAATGACCTGACCTTTAGCAGCACTTAAGGGAAAGCGCCGCTAATGACCTGACCT
TTAGCAGCTCTTAGGTA
Done.