Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000664.1 Kokia drynarioides strain JFW-HI SEQ_111651, 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: 29235
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35


Found at i:765 original size:31 final size:32

Alignment explanation


    Indices: 701--777  Score: 111
    Period size: 31  Copynumber: 2.4  Consensus size: 32

        691 TCAAAAAAGT

                        *               *   
        701 TTTAAGTACCAACTTAAAAAAAAAATATTAAG
          1 TTTAAGTACCAAATTAAAAAAAAAATATCAAG

                             *      *       
        733 TTTAAGTACCAAATT-AGAAAAAATTATCAAG
          1 TTTAAGTACCAAATTAAAAAAAAAATATCAAG

                          
        764 TTTAAGTACCAAAT
          1 TTTAAGTACCAAAT

        778 ATTATATTAA


Statistics
Matches: 41,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  31   27  0.66
  32   14  0.34

ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30


Consensus pattern (32 bp):   
TTTAAGTACCAAATTAAAAAAAAAATATCAAG

Found at i:6494 original size:28 final size:28

Alignment explanation


    Indices: 6461--6520  Score: 111
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       6451 AAAAAAAATA

                            *           
       6461 ATAAAAGTGGCATATGTAGTTAATATTG
          1 ATAAAAGTGGCATATGAAGTTAATATTG

                                        
       6489 ATAAAAGTGGCATATGAAGTTAATATTG
          1 ATAAAAGTGGCATATGAAGTTAATATTG

                
       6517 ATAA
          1 ATAA

       6521 TATTCAATAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   31  1.00

ACGTcount: A:0.43, C:0.03, G:0.20, T:0.33


Consensus pattern (28 bp):   
ATAAAAGTGGCATATGAAGTTAATATTG

Found at i:26537 original size:23 final size:21

Alignment explanation


    Indices: 26495--26539  Score: 54
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      26485 AGCTTTTATA

                *          *     
      26495 ATAATTTATATATTTTTAATT
          1 ATAAATTATATATTTATAATT

                                   
      26516 ATAAATTATATAGTTGTATAATT
          1 ATAAATTATATA-TT-TATAATT

             
      26539 A
          1 A

      26540 CAATCTATAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21   11  0.55
  22    2  0.10
  23    7  0.35

ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53


Consensus pattern (21 bp):   
ATAAATTATATATTTATAATT
Done.