Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014635.1 Kokia drynarioides strain JFW-HI SEQ_129674, 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: 12016
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:2187 original size:34 final size:34

Alignment explanation


    Indices: 2135--2205  Score: 88
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       2125 GTAGTTGTAA

                                 *  *  *      
       2135 TTTAATTGTCACCACATTTCCTTTGTCTTTGCAT
          1 TTTAATTGTCACCACATTTCCATTATCATTGCAT

                        **     *              
       2169 TTTAATTGTCACTGCATTTGCATTATCATTGCAT
          1 TTTAATTGTCACCACATTTCCATTATCATTGCAT

               
       2203 TTT
          1 TTT

       2206 CATTTGTTAA


Statistics
Matches: 31,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  34   31  1.00

ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51


Consensus pattern (34 bp):   
TTTAATTGTCACCACATTTCCATTATCATTGCAT

Found at i:2256 original size:69 final size:69

Alignment explanation


    Indices: 2180--2314  Score: 207
    Period size: 69  Copynumber: 2.0  Consensus size: 69

       2170 TTAATTGTCA

                                     *       *             *                 
       2180 CTGCATTTGCATTATCATTGCATTTTCATTTGTTAATGCATTAAGGATAATGCAAACTTTAAGTT
          1 CTGCATTTGCATTATCATTGCATTTCCATTTGTCAATGCATTAAGGACAATGCAAACTTTAAGTT

                
       2245 TGAG
         66 TGAG

                      *                           *   *           *          
       2249 CTGCATTTGCGTTATCATTGCATTTCCATTTGTCAATGTATTGAGGACAATGCAGACTTTAAGTT
          1 CTGCATTTGCATTATCATTGCATTTCCATTTGTCAATGCATTAAGGACAATGCAAACTTTAAGTT

             
       2314 T
         66 T

       2315 TAAGGGAATA


Statistics
Matches: 59,  Mismatches: 7, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  69   59  1.00

ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41


Consensus pattern (69 bp):   
CTGCATTTGCATTATCATTGCATTTCCATTTGTCAATGCATTAAGGACAATGCAAACTTTAAGTT
TGAG

Found at i:2833 original size:16 final size:16

Alignment explanation


    Indices: 2796--2829  Score: 54
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       2786 TCGGTCACAT

                            
       2796 AAAA-AATAGAAGAAG
          1 AAAAGAATAGAAGAAG

                            
       2811 AAAAGAATAGAA-AAG
          1 AAAAGAATAGAAGAAG

                
       2826 AAAA
          1 AAAA

       2830 AGAAATATAT


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

Matches are distributed among these distances:
  15   11  0.61
  16    7  0.39

ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06


Consensus pattern (16 bp):   
AAAAGAATAGAAGAAG

Found at i:3454 original size:37 final size:37

Alignment explanation


    Indices: 3380--3465  Score: 91
    Period size: 37  Copynumber: 2.3  Consensus size: 37

       3370 CAAATTTGCG

                       *   *                *    
       3380 CCCAAAACTGTTACCGCATGAGCAGTTCTAGATTGCA
          1 CCCAAAACTGTCACCACATGAGCAGTTCTAGAATGCA

                                 ** *    *       
       3417 CCCAAAACTGTCACCACATGATTATTTCTGGAATGCA
          1 CCCAAAACTGTCACCACATGAGCAGTTCTAGAATGCA

              *  *      
       3454 CCTAAGACTGTC
          1 CCCAAAACTGTC

       3466 GCTACATAAA


Statistics
Matches: 40,  Mismatches: 9, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  37   40  1.00

ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26


Consensus pattern (37 bp):   
CCCAAAACTGTCACCACATGAGCAGTTCTAGAATGCA

Found at i:4661 original size:24 final size:24

Alignment explanation


    Indices: 4629--4753  Score: 142
    Period size: 24  Copynumber: 5.2  Consensus size: 24

       4619 GCGTGATCAC

                                    
       4629 CAGCTAATGTACGTTTACGCTCGT
          1 CAGCTAATGTACGTTTACGCTCGT

                                    
       4653 CAGCTAATGTACGTTTACGCTCGT
          1 CAGCTAATGTACGTTTACGCTCGT

                   *   *         *  
       4677 CAGCTAAAGTATGTTTACGCTTGT
          1 CAGCTAATGTACGTTTACGCTCGT

              *  ** *         *     
       4701 CAACTTCTATACGTTTACACTCGT
          1 CAGCTAATGTACGTTTACGCTCGT

              *  **     *           
       4725 CAACTTCTGTACATTTACGCTCGT
          1 CAGCTAATGTACGTTTACGCTCGT

                 
       4749 CAGCT
          1 CAGCT

       4754 TTTCAGATAT


Statistics
Matches: 86,  Mismatches: 15, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   86  1.00

ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35


Consensus pattern (24 bp):   
CAGCTAATGTACGTTTACGCTCGT

Done.