Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015325.1 Kokia drynarioides strain JFW-HI SEQ_130371, 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: 591955
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34

Warning! 531 characters in sequence are not A, C, G, or T


File 3 of 3

Found at i:589484 original size:18 final size:18

Alignment explanation


    Indices: 589428--589485  Score: 75
    Period size: 18  Copynumber: 3.3  Consensus size: 18

     589418 TTAATATTGA

                              
     589428 ATTAACATAAAATATTAG
          1 ATTAACATAAAATATTAG

                    **        
     589446 ATTAA-ATTTAATATT-G
          1 ATTAACATAAAATATTAG

                               
     589462 AATTAACATAAAATATTAG
          1 -ATTAACATAAAATATTAG

                 
     589481 ATTAA
          1 ATTAA

     589486 ATTTAATATT


Statistics
Matches: 33,  Mismatches: 4, Indels: 6
        0.77            0.09        0.14

Matches are distributed among these distances:
  16    1  0.03
  17   13  0.39
  18   18  0.55
  19    1  0.03

ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38


Consensus pattern (18 bp):   
ATTAACATAAAATATTAG

Found at i:589584 original size:11 final size:11

Alignment explanation


    Indices: 589570--589645  Score: 52
    Period size: 11  Copynumber: 6.8  Consensus size: 11

     589560 GATAATCAAT

                       
     589570 TTAATATTAAA
          1 TTAATATTAAA

                       
     589581 TTAATA--AAA
          1 TTAATATTAAA

                       
     589590 -TAATATTAAA
          1 TTAATATTAAA

            *       *   
     589600 ATAAGTATCAAA
          1 TTAA-TATTAAA

                         
     589612 TTTAAT-TTAATA
          1 -TTAATATTAA-A

                         
     589624 TTAAACTATTAAA
          1 TT-AA-TATTAAA

            *        
     589637 ATAATATTA
          1 TTAATATTA

     589646 TTTTTGGAAT


Statistics
Matches: 52,  Mismatches: 4, Indels: 18
        0.70            0.05        0.24

Matches are distributed among these distances:
   8    5  0.10
   9    3  0.06
  10    3  0.06
  11   19  0.37
  12   12  0.23
  13    6  0.12
  14    4  0.08

ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41


Consensus pattern (11 bp):   
TTAATATTAAA

Found at i:589585 original size:20 final size:18

Alignment explanation


    Indices: 589547--589599  Score: 61
    Period size: 20  Copynumber: 2.8  Consensus size: 18

     589537 CATTAAAATA

                               
     589547 AATTTAATATTAAGATAAT
          1 AATTTAATATTAA-ATAAT

                                
     589566 CAATTTAATATTAAATTAAT
          1 -AATTTAATATTAAA-TAAT

              **          
     589586 AAAATAATATTAAA
          1 AATTTAATATTAAA

     589600 ATAAGTATCA


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  19   13  0.43
  20   17  0.57

ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40


Consensus pattern (18 bp):   
AATTTAATATTAAATAAT

Done.