Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002469.1 Kokia drynarioides strain JFW-HI SEQ_114607, 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: 7804
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:31 original size:13 final size:13

Alignment explanation


    Indices: 10--43  Score: 50
    Period size: 13  Copynumber: 2.6  Consensus size: 13

          1 GACTTTGTA

                *        
         10 TTTATTTTGGACT
          1 TTTAATTTGGACT

                      *  
         23 TTTAATTTGGGCT
          1 TTTAATTTGGACT

                    
         36 TTTAATTT
          1 TTTAATTT

         44 TAAATATTAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62


Consensus pattern (13 bp):   
TTTAATTTGGACT

Found at i:77 original size:6 final size:6

Alignment explanation


    Indices: 66--150  Score: 75
    Period size: 6  Copynumber: 14.2  Consensus size: 6

         56 TTTTAAATCC

                                   **                    **          
         66 ATTTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAAA AGATAA ATTTAA
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT--AA ATTTAA ATTTAA

                     *                   **            
        115 ATTT-A ATATAA ATTTAA ATTTAA AAATAA ATTTAA A
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A

        151 CCAATTTAAA


Statistics
Matches: 61,  Mismatches: 14, Indels: 8
        0.73            0.17        0.10

Matches are distributed among these distances:
   5    7  0.11
   6   50  0.82
   8    4  0.07

ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40


Consensus pattern (6 bp):   
ATTTAA

Found at i:92 original size:17 final size:17

Alignment explanation


    Indices: 69--150  Score: 94
    Period size: 17  Copynumber: 4.6  Consensus size: 17

         59 TAAATCCATT

                             
         69 TAAATTTAAATTTAAAG
          1 TAAATTTAAATTTAAAG

            *                  
         86 CAAATTTAAATTTAAAAAG
          1 TAAATTTAAATTT--AAAG

                               
        105 ATAAATTTAAATTTAATA-
          1 -TAAATTTAAATTTAA-AG

                             *
        123 TAAATTTAAATTTAAAAA
          1 TAAATTTAAATTT-AAAG

                      
        141 TAAATTTAAA
          1 TAAATTTAAA

        151 CCAATTTAAA


Statistics
Matches: 57,  Mismatches: 2, Indels: 11
        0.81            0.03        0.16

Matches are distributed among these distances:
  17   26  0.46
  18   14  0.25
  19    5  0.09
  20   12  0.21

ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39


Consensus pattern (17 bp):   
TAAATTTAAATTTAAAG

Found at i:110 original size:37 final size:35

Alignment explanation


    Indices: 69--150  Score: 121
    Period size: 37  Copynumber: 2.3  Consensus size: 35

         59 TAAATCCATT

                                                  
         69 TAAATTTAAATTTAA-AGCAAATTTAAATTTAAAAAGA
          1 TAAATTTAAATTTAATA-CAAATTTAAATTT-AAAA-A

                             *                 
        106 TAAATTTAAATTTAATATAAATTTAAATTTAAAAA
          1 TAAATTTAAATTTAATACAAATTTAAATTTAAAAA

                      
        141 TAAATTTAAA
          1 TAAATTTAAA

        151 CCAATTTAAA


Statistics
Matches: 43,  Mismatches: 1, Indels: 4
        0.90            0.02        0.08

Matches are distributed among these distances:
  35   11  0.26
  36    4  0.09
  37   27  0.63
  38    1  0.02

ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39


Consensus pattern (35 bp):   
TAAATTTAAATTTAATACAAATTTAAATTTAAAAA

Found at i:1676 original size:37 final size:37

Alignment explanation


    Indices: 1626--1707  Score: 164
    Period size: 37  Copynumber: 2.2  Consensus size: 37

       1616 TTAAGTTCTT

                                                 
       1626 TCACATAATATAATATAGGGTAAACTACACAAAATAG
          1 TCACATAATATAATATAGGGTAAACTACACAAAATAG

                                                 
       1663 TCACATAATATAATATAGGGTAAACTACACAAAATAG
          1 TCACATAATATAATATAGGGTAAACTACACAAAATAG

                    
       1700 TCACATAA
          1 TCACATAA

       1708 CTTTCAAAAA


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   45  1.00

ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24


Consensus pattern (37 bp):   
TCACATAATATAATATAGGGTAAACTACACAAAATAG
Done.