Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001065.1 Kokia drynarioides strain JFW-HI SEQ_112315, 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: 8320
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:4639 original size:26 final size:27

Alignment explanation


    Indices: 4610--4660  Score: 70
    Period size: 26  Copynumber: 1.9  Consensus size: 27

       4600 ATACCTAAAA

                                        
       4610 AAATACTAAAT-TAACTTA-CAATTTTT
          1 AAAT-CTAAATATAACTTAGCAATTTTT

                *                    
       4636 AAATTTAAATATAACTTAGCAATTT
          1 AAATCTAAATATAACTTAGCAATTT

       4661 CAGGTTAGTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  25    5  0.23
  26   11  0.50
  27    6  0.27

ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41


Consensus pattern (27 bp):   
AAATCTAAATATAACTTAGCAATTTTT

Found at i:6589 original size:37 final size:37

Alignment explanation


    Indices: 6548--6619  Score: 144
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       6538 AATTATTTAG

                                                 
       6548 ATATACTCTTATTATTAACAATATGATATTTCGTTAA
          1 ATATACTCTTATTATTAACAATATGATATTTCGTTAA

                                               
       6585 ATATACTCTTATTATTAACAATATGATATTTCGTT
          1 ATATACTCTTATTATTAACAATATGATATTTCGTT

       6620 CAAGGTACAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   35  1.00

ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47


Consensus pattern (37 bp):   
ATATACTCTTATTATTAACAATATGATATTTCGTTAA

Found at i:6607 original size:20 final size:20

Alignment explanation


    Indices: 6548--6608  Score: 58
    Period size: 20  Copynumber: 3.2  Consensus size: 20

       6538 AATTATTTAG

                                
       6548 ATATACTCTTATTATTAACA
          1 ATATACTCTTATTATTAACA

                    *    **      
       6568 ATATGA-TATT-TCGTT-A-A
          1 ATAT-ACTCTTATTATTAACA

                                
       6585 ATATACTCTTATTATTAACA
          1 ATATACTCTTATTATTAACA

                
       6605 ATAT
          1 ATAT

       6609 GATATTTCGT


Statistics
Matches: 30,  Mismatches: 6, Indels: 10
        0.65            0.13        0.22

Matches are distributed among these distances:
  16    1  0.03
  17    8  0.27
  18    4  0.13
  19    4  0.13
  20   12  0.40
  21    1  0.03

ACGTcount: A:0.39, C:0.11, G:0.03, T:0.46


Consensus pattern (20 bp):   
ATATACTCTTATTATTAACA

Found at i:6959 original size:29 final size:29

Alignment explanation


    Indices: 6925--6987  Score: 117
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       6915 TCGAATCATG

                                        *
       6925 TATCATATCAATTCCATATAGGGTATAAT
          1 TATCATATCAATTCCATATAGGGTATAAC

                                         
       6954 TATCATATCAATTCCATATAGGGTATAAC
          1 TATCATATCAATTCCATATAGGGTATAAC

                 
       6983 TATCA
          1 TATCA

       6988 CAAATGCAAA


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

Matches are distributed among these distances:
  29   33  1.00

ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37


Consensus pattern (29 bp):   
TATCATATCAATTCCATATAGGGTATAAC

Done.