Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007017.1 Kokia drynarioides strain JFW-HI SEQ_121623, 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: 11329
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36


Found at i:755 original size:27 final size:28

Alignment explanation


    Indices: 708--778  Score: 72
    Period size: 27  Copynumber: 2.6  Consensus size: 28

        698 CGGGCCAAAC

                       * *  *    *      
        708 ACAAAATAATGATATTTCGAGTCAGA-T
          1 ACAAAATAATGCTCTTCCGAGCCAGAGT

               *                        
        735 ACAGAATAATGCTCTTCCGAGCCAGAGT
          1 ACAAAATAATGCTCTTCCGAGCCAGAGT

            *       *       
        763 TCAAAATATTGCTCTT
          1 ACAAAATAATGCTCTT

        779 TTGAGCCAAA


Statistics
Matches: 35,  Mismatches: 8, Indels: 1
        0.80            0.18        0.02

Matches are distributed among these distances:
  27   21  0.60
  28   14  0.40

ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30


Consensus pattern (28 bp):   
ACAAAATAATGCTCTTCCGAGCCAGAGT

Found at i:847 original size:27 final size:27

Alignment explanation


    Indices: 722--869  Score: 109
    Period size: 27  Copynumber: 5.4  Consensus size: 27

        712 AATAATGATA

                   *    * *      *     
        722 TTTCGAGTCAGATACAGAATAATGCTC
          1 TTTCGAGCCAGAAATAGAATATTGCTC

              *         **   *          
        749 TTCCGAGCCAGAGTTCAAAATATTGCTC
          1 TTTCGAGCCAGAAAT-AGAATATTGCTC

               *      *                 
        777 TTTTGAGCCAAAAACT-GAATATTGCTC
          1 TTTCGAGCCAGAAA-TAGAATATTGCTC

               **   *   *          *   
        804 TTTTAAGCTAGATATAGAATATTTCTC
          1 TTTCGAGCCAGAAATAGAATATTGCTC

                              **  *    
        831 TTTCGAGCCAGAAATAGAGCATCGCTC
          1 TTTCGAGCCAGAAATAGAATATTGCTC

                        
        858 TTTCGAGCCAGA
          1 TTTCGAGCCAGA

        870 CTTATTGAAT


Statistics
Matches: 92,  Mismatches: 26, Indels: 6
        0.74            0.21        0.05

Matches are distributed among these distances:
  26    1  0.01
  27   71  0.77
  28   19  0.21
  29    1  0.01

ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Consensus pattern (27 bp):   
TTTCGAGCCAGAAATAGAATATTGCTC

Found at i:8099 original size:45 final size:45

Alignment explanation


    Indices: 8038--8137  Score: 182
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       8028 AGTTGGAAAT

                                                         
       8038 TTAAATAAAATGGTTAATTTGCAAGTTTTGAGCTAAAGGACTAAA
          1 TTAAATAAAATGGTTAATTTGCAAGTTTTGAGCTAAAGGACTAAA

                     *                                   
       8083 TTAAATAAACTGGTTAATTTGCAAGTTTTGAGCTAAAGGACTAAA
          1 TTAAATAAAATGGTTAATTTGCAAGTTTTGAGCTAAAGGACTAAA

              *       
       8128 TTTAATAAAA
          1 TTAAATAAAA

       8138 GTGAAAAGTT


Statistics
Matches: 52,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   52  1.00

ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34


Consensus pattern (45 bp):   
TTAAATAAAATGGTTAATTTGCAAGTTTTGAGCTAAAGGACTAAA

Found at i:8886 original size:195 final size:194

Alignment explanation


    Indices: 8480--8921  Score: 539
    Period size: 195  Copynumber: 2.3  Consensus size: 194

       8470 GAAACTGACG

                      *     *        *                *                     *
       8480 CAATGGCTGACGTACCACATATGTTACGAGTCCTCGACAGCTTGTGTGAAG-AGCACTGTGAGTC
          1 CAATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGT-AAGCAGCACTGTGAGTA

                  *                         * *      **               *    * 
       8544 GAGAAATGAGAAAAGAATCCAAGAATGGATTATATGTCCTATGATGGCTGAGATTTATTCTAAGT
         65 GAGAAACGAGAAAAGAATCCAAGAATGGATTACAGGTCCTACAATGGCTGAGATTTATGCTAAAT

                                       *                                * *  
       8609 GAATATTATCAACAACTCGTGCCAGCAGCATCGTTAGAAAACAGTTATATGCACAGATATTGTAT
        130 GAATATTATCAACAACTCGTGCCAGCAACATCGTTAGAAAACAGTTATATGCACAGATATCGCAT

                                                           *                 
       8674 CAATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTCAGCAGCA-TCGTGAGTT
          1 CAATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTAAGCAGCACT-GTGAG-T

                                                   *        *  *             
       8738 AG-GAAACGAGAAAAGAATCCAAGAATGGATTACAGGTCTTACAATGGTTGGGATTTATGCATAA
         64 AGAGAAACGAGAAAAGAATCCAAGAATGGATTACAGGTCCTACAATGGCTGAGATTTATGC-TAA

               *     * **          **              **                        
       8802 ATGCATATTCTTGACAACTCGTGTGAGCAACATCGTTAGGGAACAGTTATATGCACAGATATCGC
        128 ATGAATATTATCAACAACTCGTGCCAGCAACATCGTTAGAAAACAGTTATATGCACAGATATCGC

              
       8867 AT
        193 AT

             *                         *         *     *   *     
       8869 CGATGGCTGAGGTACCGCATATGTTGCTAGTCCTCGATAGCTCATGTGAGCAG
          1 CAATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTAAGCAG

       8922 TATCAAGTAC


Statistics
Matches: 212,  Mismatches: 32, Indels: 7
        0.84            0.13        0.03

Matches are distributed among these distances:
 193    3  0.01
 194  101  0.48
 195  108  0.51

ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26


Consensus pattern (194 bp):   
CAATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTAAGCAGCACTGTGAGTAG
AGAAACGAGAAAAGAATCCAAGAATGGATTACAGGTCCTACAATGGCTGAGATTTATGCTAAATG
AATATTATCAACAACTCGTGCCAGCAACATCGTTAGAAAACAGTTATATGCACAGATATCGCAT

Found at i:9723 original size:21 final size:21

Alignment explanation


    Indices: 9699--9754  Score: 69
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       9689 CTAGAGTTTG

                            *     
       9699 TTGTATCGGTAGAAGTGATGA-
          1 TTGTATCGGTAGAAGTCAT-AC

                *       *        
       9720 TTGTTTCGGTAGTAGTCATAC
          1 TTGTATCGGTAGAAGTCATAC

                          
       9741 TTGTATCGGTAGAA
          1 TTGTATCGGTAGAA

       9755 CTATCACAAC


Statistics
Matches: 29,  Mismatches: 5, Indels: 2
        0.81            0.14        0.06

Matches are distributed among these distances:
  20    1  0.03
  21   28  0.97

ACGTcount: A:0.25, C:0.09, G:0.29, T:0.38


Consensus pattern (21 bp):   
TTGTATCGGTAGAAGTCATAC
Done.