Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000041.1 Kokia drynarioides strain JFW-HI SEQ_75250, 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: 3703
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39


Found at i:1165 original size:15 final size:14

Alignment explanation


    Indices: 1144--1183  Score: 53
    Period size: 16  Copynumber: 2.7  Consensus size: 14

       1134 ATAATATTAT

                          
       1144 AAAATATAAAAATC
          1 AAAATATAAAAATC

                           *
       1158 AAATATATTAAAAATT
          1 AAA-ATA-TAAAAATC

                      
       1174 AAAATATAAA
          1 AAAATATAAA

       1184 GATTAAATCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  14    7  0.30
  15    6  0.26
  16   10  0.43

ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28


Consensus pattern (14 bp):   
AAAATATAAAAATC

Found at i:2042 original size:18 final size:18

Alignment explanation


    Indices: 2016--2052  Score: 65
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       2006 GCTCTAATTT

                              
       2016 TCTAATTGTTAGATCAAC
          1 TCTAATTGTTAGATCAAC

                *             
       2034 TCTAGTTGTTAGATCAAC
          1 TCTAATTGTTAGATCAAC

             
       2052 T
          1 T

       2053 TGAAAATTCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41


Consensus pattern (18 bp):   
TCTAATTGTTAGATCAAC

Found at i:2746 original size:28 final size:28

Alignment explanation


    Indices: 2714--2772  Score: 82
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       2704 TTTTAGTTAT

                          *             
       2714 TTTATAAATTTATATTTTTTTTTATAAA
          1 TTTATAAATTTATAATTTTTTTTATAAA

                   *   *              * 
       2742 TTTATAACTTTTTAATTTTTTTTATATA
          1 TTTATAAATTTATAATTTTTTTTATAAA

               
       2770 TTT
          1 TTT

       2773 TTGTATTTTT


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  28   27  1.00

ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68


Consensus pattern (28 bp):   
TTTATAAATTTATAATTTTTTTTATAAA

Found at i:2753 original size:20 final size:20

Alignment explanation


    Indices: 2713--2754  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       2703 ATTTTAGTTA

                           **   
       2713 TTTTATAAATTTATATTTTT
          1 TTTTATAAATTTATAACTTT

                                
       2733 TTTTATAAATTTATAACTTT
          1 TTTTATAAATTTATAACTTT

              
       2753 TT
          1 TT

       2755 AATTTTTTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67


Consensus pattern (20 bp):   
TTTTATAAATTTATAACTTT

Found at i:2864 original size:19 final size:19

Alignment explanation


    Indices: 2820--2865  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       2810 ATTTATATAT

                         *     
       2820 TATATATAATAAATTTTTA
          1 TATATATAATAAACTTTTA

            * *    *           
       2839 AAAATATCATAAACTTTTA
          1 TATATATAATAAACTTTTA

                    
       2858 TATATATA
          1 TATATATA

       2866 TTTATACATT


Statistics
Matches: 20,  Mismatches: 7, Indels: 0
        0.74            0.26        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46


Consensus pattern (19 bp):   
TATATATAATAAACTTTTA
Done.