Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001005.1 Kokia drynarioides strain JFW-HI SEQ_112212, 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: 9345
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33


Found at i:2704 original size:23 final size:23

Alignment explanation


    Indices: 2678--2746  Score: 77
    Period size: 23  Copynumber: 3.0  Consensus size: 23

       2668 AGCACGTTTC

                                   
       2678 GTGCCCTCTGTTCAGCATTGTGT
          1 GTGCCCTCTGTTCAGCATTGTGT

                *    *           * 
       2701 GTGCTCTCTATTCAGCATTGTAT
          1 GTGCCCTCTGTTCAGCATTGTGT

                 *      *    *     
       2724 GTG-CTTCTGTTTAGCACTGTGT
          1 GTGCCCTCTGTTCAGCATTGTGT

             
       2746 G
          1 G

       2747 CTTCTTATTA


Statistics
Matches: 37,  Mismatches: 9, Indels: 1
        0.79            0.19        0.02

Matches are distributed among these distances:
  22   14  0.38
  23   23  0.62

ACGTcount: A:0.12, C:0.22, G:0.25, T:0.42


Consensus pattern (23 bp):   
GTGCCCTCTGTTCAGCATTGTGT

Found at i:2748 original size:20 final size:20

Alignment explanation


    Indices: 2723--2761  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2713 CAGCATTGTA

                                 
       2723 TGTGCTTCTGT-TTAGCACTG
          1 TGTGCTTCT-TATTAGCACTG

                               
       2743 TGTGCTTCTTATTAGCACT
          1 TGTGCTTCTTATTAGCACT

       2762 TGGTATGCCC


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

Matches are distributed among these distances:
  19    1  0.06
  20   17  0.94

ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46


Consensus pattern (20 bp):   
TGTGCTTCTTATTAGCACTG

Found at i:6455 original size:17 final size:17

Alignment explanation


    Indices: 6433--6483  Score: 93
    Period size: 17  Copynumber: 3.0  Consensus size: 17

       6423 TTTGCAATTC

                             
       6433 CCATTCGTGAATCTAAA
          1 CCATTCGTGAATCTAAA

                             
       6450 CCATTCGTGAATCTAAA
          1 CCATTCGTGAATCTAAA

                 *           
       6467 CCATTAGTGAATCTAAA
          1 CCATTCGTGAATCTAAA

       6484 GAATTTAAAT


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  17   33  1.00

ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29


Consensus pattern (17 bp):   
CCATTCGTGAATCTAAA

Found at i:7762 original size:204 final size:204

Alignment explanation


    Indices: 7412--7799  Score: 686
    Period size: 204  Copynumber: 1.9  Consensus size: 204

       7402 ATCTTTTGCA

                             *                 *     *                       
       7412 ACTAGTAAACACGGATATGAACATGACAAGAAGGCGAGGGAGCCCGAACCAAGATAACAATGCAG
          1 ACTAGTAAACACGGATACGAACATGACAAGAAGGCAAGGGAACCCGAACCAAGATAACAATGCAG

                                                 *      *                    
       7477 CATCAGCAAGGCCGCAACGAGACAATGAACTTTCACGGTTAGTATGTGCCGGGAGGAGGAGAGGG
         66 CATCAGCAAGGCCGCAACGAGACAATGAACTTTCACGATTAGTACGTGCCGGGAGGAGGAGAGGG

                                   *   *                                     
       7542 ACACCAAGCCAAGATGAAGATGCTGCATTAGCTTTAAGGCTGCAAAGAGAAGAAGAATTCATACT
        131 ACACCAAGCCAAGATGAAGATGCGGCACTAGCTTTAAGGCTGCAAAGAGAAGAAGAATTCATACT

                     
       7607 GGGAACCCG
        196 GGGAACCCG

                                      **                                     
       7616 ACTAGTAAACACGGATACGAACATGATGAGAAGGCAAGGGAACCCGAACCAAGATAACAATGCAG
          1 ACTAGTAAACACGGATACGAACATGACAAGAAGGCAAGGGAACCCGAACCAAGATAACAATGCAG

                        *                                                    
       7681 CATCAGCAAGGCTGCAACGAGACAATGAACTTTCACGATTAGTACGTGCCGGGAGGAGGAGAGGG
         66 CATCAGCAAGGCCGCAACGAGACAATGAACTTTCACGATTAGTACGTGCCGGGAGGAGGAGAGGG

                                                                  
       7746 ACACCAAGCCAAGATGAAGATGCGGCACTAGCTTTAAGGCTGCAAAGAGAAGAA
        131 ACACCAAGCCAAGATGAAGATGCGGCACTAGCTTTAAGGCTGCAAAGAGAAGAA

       7800 TTCATGGAGG


Statistics
Matches: 174,  Mismatches: 10, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 204  174  1.00

ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14


Consensus pattern (204 bp):   
ACTAGTAAACACGGATACGAACATGACAAGAAGGCAAGGGAACCCGAACCAAGATAACAATGCAG
CATCAGCAAGGCCGCAACGAGACAATGAACTTTCACGATTAGTACGTGCCGGGAGGAGGAGAGGG
ACACCAAGCCAAGATGAAGATGCGGCACTAGCTTTAAGGCTGCAAAGAGAAGAAGAATTCATACT
GGGAACCCG

Found at i:9318 original size:2 final size:2

Alignment explanation


    Indices: 9311--9345  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       9301 CTAGCAGAGG

                                                                
       9311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.