Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002602.1 Kokia drynarioides strain JFW-HI SEQ_114814, 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: 38936
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:19597 original size:34 final size:34

Alignment explanation


    Indices: 19554--19624  Score: 133
    Period size: 34  Copynumber: 2.1  Consensus size: 34

      19544 CCATTGTTAC

                                     *        
      19554 TACATCTCATCTCTTCCATTGCTTTGATTTTCCT
          1 TACATCTCATCTCTTCCATTGCTTTAATTTTCCT

                                              
      19588 TACATCTCATCTCTTCCATTGCTTTAATTTTCCT
          1 TACATCTCATCTCTTCCATTGCTTTAATTTTCCT

               
      19622 TAC
          1 TAC

      19625 GTTCACAAGT


Statistics
Matches: 36,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   36  1.00

ACGTcount: A:0.17, C:0.30, G:0.04, T:0.49


Consensus pattern (34 bp):   
TACATCTCATCTCTTCCATTGCTTTAATTTTCCT

Found at i:35641 original size:18 final size:17

Alignment explanation


    Indices: 35618--35651  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

      35608 TTTAAAAGAA

                              
      35618 AATCAACAAAAGATTAGT
          1 AATCAACAAAAG-TTAGT

                  *         
      35636 AATCAATAAAAGTTAG
          1 AATCAACAAAAGTTAG

      35652 AAAAATAATA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    4  0.27
  18   11  0.73

ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24


Consensus pattern (17 bp):   
AATCAACAAAAGTTAGT

Found at i:38305 original size:21 final size:21

Alignment explanation


    Indices: 38281--38352  Score: 56
    Period size: 21  Copynumber: 3.3  Consensus size: 21

      38271 AAGGTGGAAG

                                 
      38281 ATGTGGCCATTAATGGCAAAT
          1 ATGTGGCCATTAATGGCAAAT

                 * *                 
      38302 ATGTGACAATTTTAAT-GCAAAATT
          1 ATGTGGCCA--TTAATGGC-AAA-T

                        *   *   *
      38326 ATGTGGCCATTATTGGAAAAC
          1 ATGTGGCCATTAATGGCAAAT

                  
      38347 ATGTGG
          1 ATGTGG

      38353 TGGTTTGTCC


Statistics
Matches: 39,  Mismatches: 7, Indels: 10
        0.70            0.12        0.18

Matches are distributed among these distances:
  21   13  0.33
  22    9  0.23
  23    9  0.23
  24    8  0.21

ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32


Consensus pattern (21 bp):   
ATGTGGCCATTAATGGCAAAT
Done.