Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003387.1 Kokia drynarioides strain JFW-HI SEQ_116122, 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: 9707
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32


Found at i:216 original size:58 final size:59

Alignment explanation


    Indices: 104--219  Score: 162
    Period size: 58  Copynumber: 2.0  Consensus size: 59

         94 GACACCCACC

                                          *           *    ***         
        104 AAAAATACGAATAAAAAAATAATATTTTTTTATGTTTGACAAGTAATGGTCGACACCAT
          1 AAAAATACGAATAAAAAAATAATATTTTTTGATGTTTGACAACTAATAACCGACACCAT

                        *                  *                          
        163 AAAAATACGAATTAAAAAATAAT-TTTTTTGGTGTTTGACAACTAATAACCGACACCA
          1 AAAAATACGAATAAAAAAATAATATTTTTTGATGTTTGACAACTAATAACCGACACCA

        220 ACTTTCCTTC


Statistics
Matches: 50,  Mismatches: 7, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  58   28  0.56
  59   22  0.44

ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31


Consensus pattern (59 bp):   
AAAAATACGAATAAAAAAATAATATTTTTTGATGTTTGACAACTAATAACCGACACCAT

Found at i:510 original size:40 final size:38

Alignment explanation


    Indices: 444--528  Score: 107
    Period size: 40  Copynumber: 2.2  Consensus size: 38

        434 AATTTTGTAT

                            *    *                
        444 TAAAAATATTGGTATGGATTATAAATTTTAATATCCAA
          1 TAAAAATATTGGTATGCATTAAAAATTTTAATATCCAA

                       *                    *       
        482 TAAAAATATTTTGTATTGCATTAAAAATTTTAGTATCCAA
          1 TAAAAATA-TTGGTA-TGCATTAAAAATTTTAATATCCAA

             *     
        522 TGAAAAT
          1 TAAAAAT

        529 TGAGACATGA


Statistics
Matches: 40,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  38    8  0.20
  39    5  0.12
  40   27  0.68

ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40


Consensus pattern (38 bp):   
TAAAAATATTGGTATGCATTAAAAATTTTAATATCCAA

Found at i:527 original size:20 final size:19

Alignment explanation


    Indices: 466--529  Score: 65
    Period size: 19  Copynumber: 3.3  Consensus size: 19

        456 TATGGATTAT

                    *          
        466 AAATTTTAATATCCAATAA
          1 AAATTTTAGTATCCAATAA

                    *     *  *   
        485 AAATATTTTGTATTGCATTAA
          1 AAAT-TTTAGTA-TCCAATAA

                             * 
        506 AAATTTTAGTATCCAATGA
          1 AAATTTTAGTATCCAATAA

                 
        525 AAATT
          1 AAATT

        530 GAGACATGAG


Statistics
Matches: 35,  Mismatches: 8, Indels: 4
        0.74            0.17        0.09

Matches are distributed among these distances:
  19   14  0.40
  20   11  0.31
  21   10  0.29

ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41


Consensus pattern (19 bp):   
AAATTTTAGTATCCAATAA

Found at i:1942 original size:58 final size:58

Alignment explanation


    Indices: 1852--1970  Score: 202
    Period size: 58  Copynumber: 2.1  Consensus size: 58

       1842 TAACTGTATC

                     *                              *                 
       1852 TACCTCAAGTAAATAACATACAACAGCAGTATAACCAATGGCTTCCAAGTTCTAATGA
          1 TACCTCAAGCAAATAACATACAACAGCAGTATAACCAATGCCTTCCAAGTTCTAATGA

                  *                                *                  
       1910 TACCTCGAGCAAATAACATACAACAGCAGTATAACCAATTCCTTCCAAGTTCTAATGA
          1 TACCTCAAGCAAATAACATACAACAGCAGTATAACCAATGCCTTCCAAGTTCTAATGA

               
       1968 TAC
          1 TAC

       1971 TAGGTCAAAG


Statistics
Matches: 57,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  58   57  1.00

ACGTcount: A:0.40, C:0.24, G:0.11, T:0.24


Consensus pattern (58 bp):   
TACCTCAAGCAAATAACATACAACAGCAGTATAACCAATGCCTTCCAAGTTCTAATGA

Found at i:9059 original size:32 final size:31

Alignment explanation


    Indices: 9023--9086  Score: 83
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       9013 TAAGGATAGA

                                            
       9023 TGTAAAAATTATACATAAATTTTAATTTAATG
          1 TGTAAAAA-TATACATAAATTTTAATTTAATG

                 **        *           *   
       9055 TGTAATTATATACATGAATTTTAATTTGATG
          1 TGTAAAAATATACATAAATTTTAATTTAATG

             
       9086 T
          1 T

       9087 AATTATACAC


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  31   22  0.79
  32    6  0.21

ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47


Consensus pattern (31 bp):   
TGTAAAAATATACATAAATTTTAATTTAATG

Found at i:9069 original size:31 final size:29

Alignment explanation


    Indices: 9032--9093  Score: 88
    Period size: 31  Copynumber: 2.1  Consensus size: 29

       9022 ATGTAAAAAT

                                           
       9032 TATACATAAATTTTAATTTAATGTGTAATTA
          1 TATACATAAATTTTAATTTAA--TGTAATTA

                   *           *         
       9063 TATACATGAATTTTAATTTGATGTAATTA
          1 TATACATAAATTTTAATTTAATGTAATTA

              
       9092 TA
          1 TA

       9094 CACGTTAAAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  29   10  0.34
  31   19  0.66

ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48


Consensus pattern (29 bp):   
TATACATAAATTTTAATTTAATGTAATTA
Done.