Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011255.1 Kokia drynarioides strain JFW-HI SEQ_126233, 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: 1791
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35


Found at i:448 original size:24 final size:24

Alignment explanation


    Indices: 366--450  Score: 75
    Period size: 24  Copynumber: 3.6  Consensus size: 24

        356 ACTCGTATGT

                 *                   
        366 GTTTATGCTCG-CTAGCTTGCACAC
          1 GTTTACGCTCGTC-AGCTTGCACAC

                        *     ** *  
        390 GTTTACGCTCGTTAGCTTATATAC
          1 GTTTACGCTCGTCAGCTTGCACAC

             *     *                
        414 -ATTACGGTCGTCAGCTTGCACAC
          1 GTTTACGCTCGTCAGCTTGCACAC

                   *      
        437 GTTTACGTTCGTCA
          1 GTTTACGCTCGTCA

        451 TTTACGCTCA


Statistics
Matches: 46,  Mismatches: 13, Indels: 4
        0.73            0.21        0.06

Matches are distributed among these distances:
  23   17  0.37
  24   29  0.63

ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35


Consensus pattern (24 bp):   
GTTTACGCTCGTCAGCTTGCACAC

Found at i:481 original size:24 final size:24

Alignment explanation


    Indices: 449--515  Score: 107
    Period size: 24  Copynumber: 2.8  Consensus size: 24

        439 TTACGTTCGT

                       *            
        449 CATTTACGCTCATCAGCTTATATA
          1 CATTTACGCTCGTCAGCTTATATA

                                    
        473 CATTTACGCTCGTCAGCTTATATA
          1 CATTTACGCTCGTCAGCTTATATA

             *        *        
        497 CGTTTACGCTTGTCAGCTT
          1 CATTTACGCTCGTCAGCTT

        516 GCACACGTTT


Statistics
Matches: 40,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   40  1.00

ACGTcount: A:0.22, C:0.25, G:0.13, T:0.39


Consensus pattern (24 bp):   
CATTTACGCTCGTCAGCTTATATA

Found at i:523 original size:24 final size:24

Alignment explanation


    Indices: 475--552  Score: 102
    Period size: 24  Copynumber: 3.2  Consensus size: 24

        465 CTTATATACA

                    *        ** *   
        475 TTTACGCTCGTCAGCTTATATACG
          1 TTTACGCTTGTCAGCTTGCACACG

                                    
        499 TTTACGCTTGTCAGCTTGCACACG
          1 TTTACGCTTGTCAGCTTGCACACG

                 *       *          
        523 TTTACACTTGTCAACTTGCACACG
          1 TTTACGCTTGTCAGCTTGCACACG

                  
        547 TTTACG
          1 TTTACG

        553 TGATTCAATG


Statistics
Matches: 47,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   47  1.00

ACGTcount: A:0.21, C:0.27, G:0.17, T:0.36


Consensus pattern (24 bp):   
TTTACGCTTGTCAGCTTGCACACG

Found at i:977 original size:44 final size:44

Alignment explanation


    Indices: 929--1018  Score: 171
    Period size: 44  Copynumber: 2.0  Consensus size: 44

        919 CATTGCCTTC

                                                        
        929 CAAATCCATAATAAATTTAAAATCAATTACCCACGACAATCATT
          1 CAAATCCATAATAAATTTAAAATCAATTACCCACGACAATCATT

                              *                         
        973 CAAATCCATAATAAATTTTAAATCAATTACCCACGACAATCATT
          1 CAAATCCATAATAAATTTAAAATCAATTACCCACGACAATCATT

              
       1017 CA
          1 CA

       1019 TTTATGGTAA


Statistics
Matches: 45,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  44   45  1.00

ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28


Consensus pattern (44 bp):   
CAAATCCATAATAAATTTAAAATCAATTACCCACGACAATCATT

Found at i:1323 original size:23 final size:23

Alignment explanation


    Indices: 1280--1323  Score: 70
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1270 CCTTCCCTTC

                         *  *      
       1280 CTTTCTTTTTATTCTTTTAATTT
          1 CTTTCTTTTTATTATTATAATTT

                                 
       1303 CTTTCTTTTTATTATTATAAT
          1 CTTTCTTTTTATTATTATAAT

       1324 CTCTAAACAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.18, C:0.11, G:0.00, T:0.70


Consensus pattern (23 bp):   
CTTTCTTTTTATTATTATAATTT
Done.