Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012323.1 Kokia drynarioides strain JFW-HI SEQ_127325, 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: 4369
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33


Found at i:1125 original size:72 final size:72

Alignment explanation


    Indices: 845--1098  Score: 420
    Period size: 72  Copynumber: 3.5  Consensus size: 72

        835 AACAAATTTT

                      *     *             *        **    *                   
        845 ATATCCAAAATC-AAATATAAACAACTATTAATAAAACTAAATTACACATAAATAAGTAGAACAT
          1 ATATCCAAAAACTAAACATAAACAACTATTGATAAAACTTGATTATACATAAATAAGTAGAACAT

                 * 
        909 AAATTTA
         66 AAATTCA

                        *                                                    
        916 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTTGATTATACATAAATAAGTAGAACAT
          1 ATATCCAAAAACTAAACATAAACAACTATTGATAAAACTTGATTATACATAAATAAGTAGAACAT

                   
        981 AAATTCA
         66 AAATTCA

                                                                             
        988 ATATCCAAAAACTAAACATAAACAACTATTGATAAAACTTGATTATACATAAATAAGTAGAACAT
          1 ATATCCAAAAACTAAACATAAACAACTATTGATAAAACTTGATTATACATAAATAAGTAGAACAT

                   
       1053 AAATTCA
         66 AAATTCA

                                     *             
       1060 ATATCCAAAAACTAAACATAAACAATTATTGATAAAACT
          1 ATATCCAAAAACTAAACATAAACAACTATTGATAAAACT

       1099 AGTTTAGCAT


Statistics
Matches: 173,  Mismatches: 9, Indels: 1
        0.95            0.05        0.01

Matches are distributed among these distances:
  71   11  0.06
  72  162  0.94

ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26


Consensus pattern (72 bp):   
ATATCCAAAAACTAAACATAAACAACTATTGATAAAACTTGATTATACATAAATAAGTAGAACAT
AAATTCA

Found at i:2924 original size:22 final size:21

Alignment explanation


    Indices: 2883--2924  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2873 CTGAGGAAAA

                      *          
       2883 ATAAAAGAAACGAAATTAAAG
          1 ATAAAAGAAAAGAAATTAAAG

                       *         
       2904 ATAAAAGAAAATAGAATTAAA
          1 ATAAAAGAAAAGA-AATTAAA

       2925 AGAAATATAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21   11  0.61
  22    7  0.39

ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17


Consensus pattern (21 bp):   
ATAAAAGAAAAGAAATTAAAG

Found at i:3762 original size:19 final size:19

Alignment explanation


    Indices: 3738--3780  Score: 52
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       3728 AAAATTAAAT

                                
       3738 TAAATACAAAT-TTAAATAA
          1 TAAATA-AAATCTTAAATAA

                   *          *
       3757 TAAATAATATCTTAAATAT
          1 TAAATAAAATCTTAAATAA

                 
       3776 TAAAT
          1 TAAAT

       3781 CCTAATAAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  18    3  0.14
  19   18  0.86

ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37


Consensus pattern (19 bp):   
TAAATAAAATCTTAAATAA

Found at i:4059 original size:4 final size:4

Alignment explanation


    Indices: 4050--4110  Score: 113
    Period size: 4  Copynumber: 15.2  Consensus size: 4

       4040 ATTAGATGAT

                                                                      *
       4050 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA
          1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG

                            
       4098 TATG TATG TATG T
          1 TATG TATG TATG T

       4111 TTGACAGTAA


Statistics
Matches: 55,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   4   55  1.00

ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51


Consensus pattern (4 bp):   
TATG

Done.