Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001872.1 Kokia drynarioides strain JFW-HI SEQ_113638, 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, 631

Length: 1053
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.44


Found at i:604 original size:23 final size:22

Alignment explanation


    Indices: 578--652  Score: 79
    Period size: 20  Copynumber: 3.5  Consensus size: 22

        568 ATTATATTGT

                                   
        578 TGTTTTGGTATTGTTTTTTTTAC
          1 TGTTTTGGT-TTGTTTTTTTTAC

                                   
        601 TGTTTTGG-TTGCTTTTTTTT--
          1 TGTTTTGGTTTG-TTTTTTTTAC

                                    
        621 TGTTGTT--TTTGTGTTTTTTTAC
          1 TGTT-TTGGTTTGT-TTTTTTTAC

                      
        643 TGTTTTGGTT
          1 TGTTTTGGTT

        653 GCTATTTTCA


Statistics
Matches: 44,  Mismatches: 0, Indels: 16
        0.73            0.00        0.27

Matches are distributed among these distances:
  19    1  0.02
  20   14  0.32
  21    7  0.16
  22   12  0.27
  23   10  0.23

ACGTcount: A:0.04, C:0.04, G:0.20, T:0.72


Consensus pattern (22 bp):   
TGTTTTGGTTTGTTTTTTTTAC

Found at i:618 original size:20 final size:20

Alignment explanation


    Indices: 593--660  Score: 64
    Period size: 20  Copynumber: 3.2  Consensus size: 20

        583 TGGTATTGTT

                                
        593 TTTTTTACTGTTTTGGTTGC
          1 TTTTTTACTGTTTTGGTTGC

                  **       **    *
        613 TTTTTTTTTGTTGTTTTTGTGT
          1 TTTTTTACTGTT-TTGGT-TGC

                                
        635 TTTTTTACTGTTTTGGTTGC
          1 TTTTTTACTGTTTTGGTTGC

                  
        655 TATTTT
          1 T-TTTT

        661 CATGTTATTT


Statistics
Matches: 35,  Mismatches: 10, Indels: 5
        0.70            0.20        0.10

Matches are distributed among these distances:
  20   13  0.37
  21   10  0.29
  22   12  0.34

ACGTcount: A:0.04, C:0.06, G:0.18, T:0.72


Consensus pattern (20 bp):   
TTTTTTACTGTTTTGGTTGC

Found at i:689 original size:12 final size:12

Alignment explanation


    Indices: 663--769  Score: 91
    Period size: 12  Copynumber: 9.3  Consensus size: 12

        653 GCTATTTTCA

                       *
        663 TGTTA-TTTTGC
          1 TGTTATTTTTGT

                        
        674 TGTTATTTTTGT
          1 TGTTATTTTTGT

                        
        686 TGTTATTTTTGT
          1 TGTTATTTTTGT

                        
        698 TGTTATTTTTGT
          1 TGTTATTTTTGT

                     *   
        710 TGTT-TTTAATGT
          1 TGTTATTT-TTGT

                       *
        722 TG----TTTTGC
          1 TGTTATTTTTGT

                       *
        730 TGTTATTTTTGC
          1 TGTTATTTTTGT

              * *       
        742 TGCTGTTTTTGT
          1 TGTTATTTTTGT

             * *        
        754 TATCATTTTTGT
          1 TGTTATTTTTGT

                
        766 TGTT
          1 TGTT

        770 TGGATATTAT


Statistics
Matches: 77,  Mismatches: 13, Indels: 11
        0.76            0.13        0.11

Matches are distributed among these distances:
   8    4  0.05
   9    2  0.03
  11    8  0.10
  12   63  0.82

ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69


Consensus pattern (12 bp):   
TGTTATTTTTGT

Found at i:722 original size:56 final size:56

Alignment explanation


    Indices: 657--770  Score: 165
    Period size: 56  Copynumber: 2.0  Consensus size: 56

        647 TTGGTTGCTA

                *                       *  *          * *           
        657 TTTTCATGTTATTTTGCTGTTATTTTTGTTGTTATTTTTGTTGTTATTTTTGTTGT
          1 TTTTAATGTTATTTTGCTGTTATTTTTGCTGCTATTTTTGTTATCATTTTTGTTGT

                      *                      *                      
        713 TTTTAATGTTGTTTTGCTGTTATTTTTGCTGCTGTTTTTGTTATCATTTTTGTTGT
          1 TTTTAATGTTATTTTGCTGTTATTTTTGCTGCTATTTTTGTTATCATTTTTGTTGT

              
        769 TT
          1 TT

        771 GGATATTATT


Statistics
Matches: 51,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  56   51  1.00

ACGTcount: A:0.09, C:0.05, G:0.17, T:0.69


Consensus pattern (56 bp):   
TTTTAATGTTATTTTGCTGTTATTTTTGCTGCTATTTTTGTTATCATTTTTGTTGT

Found at i:927 original size:16 final size:15

Alignment explanation


    Indices: 895--924  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        885 TCTTAATATA

                           
        895 AAATTTATGTATTTT
          1 AAATTTATGTATTTT

                    *      
        910 AAATTTATTTATTTT
          1 AAATTTATGTATTTT

        925 TAATGTTTGT


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63


Consensus pattern (15 bp):   
AAATTTATGTATTTT
Done.