Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014474.1 Kokia drynarioides strain JFW-HI SEQ_129513, 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: 14813
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:92 original size:23 final size:22

Alignment explanation


    Indices: 51--121  Score: 65
    Period size: 23  Copynumber: 3.1  Consensus size: 22

         41 TAAGTATATG

                                  
         51 TTTAA-TTATTTTTTAATTTAA
          1 TTTAATTTATTTTTTAATTTAA

                            *    * 
         72 TTTAATTTAATTTTTTTATTTTA
          1 TTTAATTT-ATTTTTTAATTTAA

               *                     
         95 TTTTATTT-TTTATTTAATGTTATA
          1 TTTAATTTATTT-TTTAAT-TTA-A

               
        119 TTT
          1 TTT

        122 TCCATGTTTG


Statistics
Matches: 40,  Mismatches: 5, Indels: 7
        0.77            0.10        0.13

Matches are distributed among these distances:
  21    8  0.20
  22    7  0.17
  23   21  0.52
  24    4  0.10

ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72


Consensus pattern (22 bp):   
TTTAATTTATTTTTTAATTTAA

Found at i:94 original size:19 final size:18

Alignment explanation


    Indices: 71--122  Score: 61
    Period size: 17  Copynumber: 2.8  Consensus size: 18

         61 TTTTAATTTA

                              
         71 ATTTAATTTAATTTTTTT
          1 ATTTAATTTAATTTTTTT

                *    *        
         89 ATTTTATTTTA-TTTTTT
          1 ATTTAATTTAATTTTTTT

                             
        106 ATTTAATGTTATATTTT
          1 ATTTAAT-TTA-ATTTT

        123 CCATGTTTGC


Statistics
Matches: 27,  Mismatches: 4, Indels: 4
        0.77            0.11        0.11

Matches are distributed among these distances:
  17   12  0.44
  18   11  0.41
  19    1  0.04
  20    3  0.11

ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73


Consensus pattern (18 bp):   
ATTTAATTTAATTTTTTT

Found at i:120 original size:24 final size:23

Alignment explanation


    Indices: 56--122  Score: 65
    Period size: 19  Copynumber: 3.1  Consensus size: 23

         46 ATATGTTTAA

                                    
         56 TTATTTTTTAATTTAATTTA-A-T
          1 TTATTTTTT-ATTTAATTTATATT

                *                  
         78 TTA-ATTTT-TTT-ATTT-TATT
          1 TTATTTTTTATTTAATTTATATT

                                    
         97 TTATTTTTTATTTAATGTTATATT
          1 TTATTTTTTATTTAAT-TTATATT

              
        121 TT
          1 TT

        123 CCATGTTTGC


Statistics
Matches: 36,  Mismatches: 2, Indels: 12
        0.72            0.04        0.24

Matches are distributed among these distances:
  18    5  0.14
  19    7  0.19
  20    4  0.11
  21    7  0.19
  22    5  0.14
  23    2  0.06
  24    6  0.17

ACGTcount: A:0.25, C:0.00, G:0.01, T:0.73


Consensus pattern (23 bp):   
TTATTTTTTATTTAATTTATATT

Found at i:1882 original size:31 final size:31

Alignment explanation


    Indices: 1819--1882  Score: 83
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       1809 TTAGACCTTC

                   *         *  *     *    
       1819 AACTTGATAATTATTTTCATGTTGAAGCTTA
          1 AACTTGACAATTATTTTAATATTGAAACTTA

                                       *   
       1850 AACTTGACAATTATTTTAATATTGAAATTTA
          1 AACTTGACAATTATTTTAATATTGAAACTTA

              
       1881 AA
          1 AA

       1883 TTTTAGAGTT


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44


Consensus pattern (31 bp):   
AACTTGACAATTATTTTAATATTGAAACTTA

Found at i:12482 original size:19 final size:19

Alignment explanation


    Indices: 12458--12495  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      12448 ACTATCATTG

                               
      12458 TACAATACCCAAACCCAAC
          1 TACAATACCCAAACCCAAC

                     *  *      
      12477 TACAATACCGAAGCCCAAC
          1 TACAATACCCAAACCCAAC

      12496 ACCATCGTCG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.45, C:0.39, G:0.05, T:0.11


Consensus pattern (19 bp):   
TACAATACCCAAACCCAAC
Done.