Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015163.1 Kokia drynarioides strain JFW-HI SEQ_130207, 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: 290727
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33

Warning! 107 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:278927 original size:25 final size:26

Alignment explanation


    Indices: 278862--278927  Score: 75
    Period size: 25  Copynumber: 2.6  Consensus size: 26

     278852 TCCTAAGGAT

                                      
     278862 TTGCCACAAAGG-TTTTACAGAGAAA
          1 TTGCCACAAAGGCTTTTACAGAGAAA

             **                      * 
     278887 TCACCAC-AAGGTCTTTT-CAGAGAGA
          1 TTGCCACAAAGG-CTTTTACAGAGAAA

                            
     278912 TTGCCACAAAGGCTTT
          1 TTGCCACAAAGGCTTT

     278928 CTAGATAGAT


Statistics
Matches: 33,  Mismatches: 5, Indels: 6
        0.75            0.11        0.14

Matches are distributed among these distances:
  24    4  0.12
  25   21  0.64
  26    8  0.24

ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26


Consensus pattern (26 bp):   
TTGCCACAAAGGCTTTTACAGAGAAA

Found at i:278973 original size:35 final size:35

Alignment explanation


    Indices: 278927--278997  Score: 124
    Period size: 35  Copynumber: 2.0  Consensus size: 35

     278917 ACAAAGGCTT

                                               
     278927 TCTAGATAGATCCTTGTTTATGTCCCGACGGACCA
          1 TCTAGATAGATCCTTGTTTATGTCCCGACGGACCA

                                    *  *       
     278962 TCTAGATAGATCCTTGTTTATGTCTCGGCGGACCA
          1 TCTAGATAGATCCTTGTTTATGTCCCGACGGACCA

             
     278997 T
          1 T

     278998 TTTTGTGGAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  35   34  1.00

ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34


Consensus pattern (35 bp):   
TCTAGATAGATCCTTGTTTATGTCCCGACGGACCA

Found at i:283073 original size:26 final size:26

Alignment explanation


    Indices: 283044--283100  Score: 87
    Period size: 26  Copynumber: 2.2  Consensus size: 26

     283034 TATCAAGGAC

                              *   *   
     283044 AAAATCGTTAAAATTTTATTAGGGGT
          1 AAAATCGTTAAAATTTTACTAGAGGT

                             *        
     283070 AAAATCGTTAAAATTTTGCTAGAGGT
          1 AAAATCGTTAAAATTTTACTAGAGGT

                 
     283096 AAAAT
          1 AAAAT

     283101 AAGGATGAGA


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  26   28  1.00

ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35


Consensus pattern (26 bp):   
AAAATCGTTAAAATTTTACTAGAGGT

Found at i:286609 original size:3 final size:3

Alignment explanation


    Indices: 286603--286628  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

     286593 ATAATAATAA

                                              
     286603 TAT TAT TAT TAT TAT TAT TAT TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TA

     286629 AATATAAAAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
TAT

Found at i:289316 original size:15 final size:15

Alignment explanation


    Indices: 289289--289317  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

     289279 ATTTATCCAC

                           
     289289 ACCATTATGAAAAAA
          1 ACCATTATGAAAAAA

                           
     289304 ACCA-TATGAAAAAA
          1 ACCATTATGAAAAAA

     289318 TAACATAATC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17


Consensus pattern (15 bp):   
ACCATTATGAAAAAA

Done.