Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008081.1 Kokia drynarioides strain JFW-HI SEQ_122737, 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: 5215
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34


Found at i:4719 original size:26 final size:26

Alignment explanation


    Indices: 4683--4740  Score: 71
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       4673 TCGGGTCTTC

                *                 *   
       4683 CAGAATTTAGCTCATACAAGCCTAAA
          1 CAGAGTTTAGCTCATACAAGCCCAAA

                        **     *      
       4709 CAGAGTTTAGCTTTTACAATCCCAAA
          1 CAGAGTTTAGCTCATACAAGCCCAAA

                  
       4735 CAGAGT
          1 CAGAGT

       4741 ATAACCAGTA


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26


Consensus pattern (26 bp):   
CAGAGTTTAGCTCATACAAGCCCAAA

Found at i:4928 original size:80 final size:82

Alignment explanation


    Indices: 4755--4942  Score: 220
    Period size: 80  Copynumber: 2.3  Consensus size: 82

       4745 CCAGTATACG

                              *                              **    *         
       4755 ATGCTGCTCACACAAGCTGT-AAGAAAACTGCAACATATGCAAGATCCCTGCCATTGATACGGTC
          1 ATGCTGCTCACACAAGCTATCAAGAAAACTGCAACATATGCAAGATCCCAACCATCGATACGGTC

                             
       4819 CATATTACCCAGTCACA
         66 CATATTACCCAGTCACA

               *  *        *          **   *               *            *    
       4836 ATGTTGTTCACACAACCTATCAAGAATTC-GTAACATATGCAAGATCTCAACCATCG-TAGGGTC
          1 ATGCTGCTCACACAAGCTATCAAGAAAACTGCAACATATGCAAGATCCCAACCATCGATACGGTC

               *     *     * 
       4899 CATGTTACCTAGTCATA
         66 CATATTACCCAGTCACA

                                       
       4916 ATGCTGCTCACACAAGCTATCAAGAAA
          1 ATGCTGCTCACACAAGCTATCAAGAAA

       4943 TTGCAGCGTA


Statistics
Matches: 87,  Mismatches: 19, Indels: 3
        0.80            0.17        0.03

Matches are distributed among these distances:
  80   43  0.49
  81   38  0.44
  82    6  0.07

ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24


Consensus pattern (82 bp):   
ATGCTGCTCACACAAGCTATCAAGAAAACTGCAACATATGCAAGATCCCAACCATCGATACGGTC
CATATTACCCAGTCACA

Found at i:4979 original size:80 final size:80

Alignment explanation


    Indices: 4755--4975  Score: 189
    Period size: 80  Copynumber: 2.8  Consensus size: 80

       4745 CCAGTATACG

                           *  *       **                   * **    *  * *    
       4755 ATGCTGCTCACACAAGCTGT-AAGAAAACTGCAACATATGCAAGATCCCTGCCATTGATACGGTC
          1 ATGCTGCTCACACAACCTATCAAGAATTC-GCAACATATGCAAGATCTCAACCATCG-CAGGGTC

                             
       4819 CATATTACCCAGTCACA
         64 CATATTACCCAGTCACA

               *  *                       *                         *        
       4836 ATGTTGTTCACACAACCTATCAAGAATTCGTAACATATGCAAGATCTCAACCATCGTAGGGTCCA
          1 ATGCTGCTCACACAACCTATCAAGAATTCGCAACATATGCAAGATCTCAACCATCGCAGGGTCCA

             *     *     * 
       4901 TGTTACCTAGTCATA
         66 TATTACCCAGTCACA

                           *                 * *      *                    
       4916 ATGCTGCTCACACAAGCTATCAAGAAATT-GCAGCGTA-GCAGGATCAT-AACCATCGCAGGG
          1 ATGCTGCTCACACAACCTATCAAG-AATTCGCAACATATGCAAGATC-TCAACCATCGCAGGG

       4976 GTCCTTACAA


Statistics
Matches: 114,  Mismatches: 23, Indels: 8
        0.79            0.16        0.06

Matches are distributed among these distances:
  79   19  0.17
  80   47  0.41
  81   42  0.37
  82    6  0.05

ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24


Consensus pattern (80 bp):   
ATGCTGCTCACACAACCTATCAAGAATTCGCAACATATGCAAGATCTCAACCATCGCAGGGTCCA
TATTACCCAGTCACA
Done.