Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004969.1 Kokia drynarioides strain JFW-HI SEQ_118700, 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: 32753
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:10802 original size:20 final size:19

Alignment explanation


    Indices: 10762--10804  Score: 59
    Period size: 20  Copynumber: 2.2  Consensus size: 19

      10752 CAAGATATTA

                            *  
      10762 TTTTTAAATCTTTTAATAT
          1 TTTTTAAATCTTTTAAGAT

                            *   
      10781 TTTTTACAATCTTTTACGAT
          1 TTTTTA-AATCTTTTAAGAT

                
      10801 TTTT
          1 TTTT

      10805 AATAAGCTTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19    6  0.29
  20   15  0.71

ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63


Consensus pattern (19 bp):   
TTTTTAAATCTTTTAAGAT

Found at i:11629 original size:31 final size:31

Alignment explanation


    Indices: 11594--11652  Score: 75
    Period size: 31  Copynumber: 1.9  Consensus size: 31

      11584 TTTCAAAAAG

                                            
      11594 TTACAAAATAA-TCATTGAAATATTTGAAGGT
          1 TTAC-AAATAAGTCATTGAAATATTTGAAGGT

                 **            *        
      11625 TTACATTTAAGTCATTGAACTATTTGAA
          1 TTACAAATAAGTCATTGAAATATTTGAA

      11653 AATTTTATTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  30    4  0.17
  31   20  0.83

ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39


Consensus pattern (31 bp):   
TTACAAATAAGTCATTGAAATATTTGAAGGT

Found at i:11665 original size:30 final size:31

Alignment explanation


    Indices: 11605--11668  Score: 85
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      11595 TACAAAATAA

                             **            
      11605 TCATTGAAATATTTGAAGGTTTACATTTAAG
          1 TCATTGAAATATTTGAAAATTTACATTTAAG

                    *              *       
      11636 TCATTGAACTATTTGAAAATTT-TATTTAAG
          1 TCATTGAAATATTTGAAAATTTACATTTAAG

               
      11666 TCA
          1 TCA

      11669 CTGGATTGTT


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  30   10  0.34
  31   19  0.66

ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44


Consensus pattern (31 bp):   
TCATTGAAATATTTGAAAATTTACATTTAAG

Found at i:26634 original size:38 final size:38

Alignment explanation


    Indices: 26581--26659  Score: 140
    Period size: 38  Copynumber: 2.1  Consensus size: 38

      26571 TGAATTAACG

                      *     *                     
      26581 ATGTAATTAGTGCGATTCGAATTCATATCACACTTGAA
          1 ATGTAATTAGCGCGATGCGAATTCATATCACACTTGAA

                                                  
      26619 ATGTAATTAGCGCGATGCGAATTCATATCACACTTGAA
          1 ATGTAATTAGCGCGATGCGAATTCATATCACACTTGAA

               
      26657 ATG
          1 ATG

      26660 ATGAGCACGA


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   39  1.00

ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Consensus pattern (38 bp):   
ATGTAATTAGCGCGATGCGAATTCATATCACACTTGAA
Done.