Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003117.1 Kokia drynarioides strain JFW-HI SEQ_115690, 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, 691

Length: 1152
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30


Found at i:104 original size:13 final size:13

Alignment explanation


    Indices: 86--151  Score: 73
    Period size: 12  Copynumber: 5.2  Consensus size: 13

         76 ACAACATACG

                         
         86 AAATAACATTAAA
          1 AAATAACATTAAA

                       * 
         99 AAATAACA-TACA
          1 AAATAACATTAAA

                  *       
        111 AAATAATATTAAAA
          1 AAATAACATT-AAA

               *         
        125 AAACAACA-TAAA
          1 AAATAACATTAAA

                  *      
        137 AAATAATATTAAA
          1 AAATAACATTAAA

              
        150 AA
          1 AA

        152 GGGTAACTTA


Statistics
Matches: 43,  Mismatches: 7, Indels: 6
        0.77            0.12        0.11

Matches are distributed among these distances:
  12   19  0.44
  13   16  0.37
  14    8  0.19

ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21


Consensus pattern (13 bp):   
AAATAACATTAAA

Found at i:106 original size:25 final size:25

Alignment explanation


    Indices: 70--151  Score: 119
    Period size: 25  Copynumber: 3.2  Consensus size: 25

         60 TCAGACATAA

                           *      *  
         70 TAAAAAACAACATACGAAATAACAT
          1 TAAAAAACAACATACAAAATAATAT

                   *                 
         95 TAAAAAATAACATACAAAATAATAT
          1 TAAAAAACAACATACAAAATAATAT

                           *          
        120 TAAAAAAACAACATAAAAAATAATAT
          1 T-AAAAAACAACATACAAAATAATAT

                  
        146 TAAAAA
          1 TAAAAA

        152 GGGTAACTTA


Statistics
Matches: 51,  Mismatches: 5, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  25   28  0.55
  26   23  0.45

ACGTcount: A:0.70, C:0.10, G:0.01, T:0.20


Consensus pattern (25 bp):   
TAAAAAACAACATACAAAATAATAT

Found at i:113 original size:12 final size:12

Alignment explanation


    Indices: 73--116  Score: 52
    Period size: 12  Copynumber: 3.6  Consensus size: 12

         63 GACATAATAA

                *       
         73 AAAACAACATAC
          1 AAAATAACATAC

            *           *
         85 GAAATAACATTAA
          1 AAAATAACA-TAC

                        
         98 AAAATAACATAC
          1 AAAATAACATAC

                   
        110 AAAATAA
          1 AAAATAA

        117 TATTAAAAAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 2
        0.79            0.15        0.06

Matches are distributed among these distances:
  12   16  0.62
  13   10  0.38

ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16


Consensus pattern (12 bp):   
AAAATAACATAC

Found at i:125 original size:26 final size:26

Alignment explanation


    Indices: 71--151  Score: 119
    Period size: 26  Copynumber: 3.2  Consensus size: 26

         61 CAGACATAAT

                          *      *    
         71 AAAAAACAACATACGAAATAACATT-
          1 AAAAAACAACATACAAAATAATATTA

                  *                   
         96 AAAAAATAACATACAAAATAATATTA
          1 AAAAAACAACATACAAAATAATATTA

                         *            
        122 AAAAAACAACATAAAAAATAATATTA
          1 AAAAAACAACATACAAAATAATATTA

                
        148 AAAA
          1 AAAA

        152 GGGTAACTTA


Statistics
Matches: 50,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  25   22  0.44
  26   28  0.56

ACGTcount: A:0.70, C:0.10, G:0.01, T:0.19


Consensus pattern (26 bp):   
AAAAAACAACATACAAAATAATATTA
Done.