Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015356.1 Kokia drynarioides strain JFW-HI SEQ_130403, 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: 269632
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34

Warning! 115 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:253826 original size:21 final size:20

Alignment explanation


    Indices: 253785--253826  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 20

     253775 ATTCACTTAC

                  *             
     253785 ATTTTATAAAAATATTAAAA
          1 ATTTTAAAAAAATATTAAAA

                                  
     253805 ATTTTAAAAAAGATATATAAAA
          1 ATTTTAAAAAA-ATAT-TAAAA

     253827 GTTTATCCAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20   10  0.53
  21    4  0.21
  22    5  0.26

ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36


Consensus pattern (20 bp):   
ATTTTAAAAAAATATTAAAA

Found at i:254609 original size:4 final size:4

Alignment explanation


    Indices: 254595--254624  Score: 51
    Period size: 4  Copynumber: 7.5  Consensus size: 4

     254585 TTCAGAAGTG

                 *                               
     254595 AATA TATA AATA AATA AATA AATA AATA AA
          1 AATA AATA AATA AATA AATA AATA AATA AA

     254625 AAACATTATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27


Consensus pattern (4 bp):   
AATA

Found at i:258006 original size:10 final size:9

Alignment explanation


    Indices: 257990--258015  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

     257980 ATTAAACTCC

                     
     257990 CTTTTTTTT
          1 CTTTTTTTT

                     
     257999 CTTTTTTTT
          1 CTTTTTTTT

                    
     258008 CTTTTTTT
          1 CTTTTTTT

     258016 AATTTTTATC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88


Consensus pattern (9 bp):   
CTTTTTTTT

Found at i:263870 original size:20 final size:20

Alignment explanation


    Indices: 263836--263873  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

     263826 CTCAATCTAC

                     **         
     263836 GATAATTAATTATTTAATTA
          1 GATAATTAAGGATTTAATTA

                              
     263856 GATAATTAAGGATTTAAT
          1 GATAATTAAGGATTTAAT

     263874 CGATCATAGG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45


Consensus pattern (20 bp):   
GATAATTAAGGATTTAATTA

Found at i:265459 original size:16 final size:16

Alignment explanation


    Indices: 265438--265482  Score: 56
    Period size: 16  Copynumber: 2.8  Consensus size: 16

     265428 AATTAATTAA

                             
     265438 TTTTTAAT-TTTTATAT
          1 TTTTTAATATTTTAT-T

                             
     265454 TTTTTAATAATTTTATT
          1 TTTTTAAT-ATTTTATT

                   *    
     265471 TTTTTAAAATTT
          1 TTTTTAATATTT

     265483 AAAAATTAAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  16   12  0.46
  17    8  0.31
  18    6  0.23

ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71


Consensus pattern (16 bp):   
TTTTTAATATTTTATT

Done.