Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011917.1 Kokia drynarioides strain JFW-HI SEQ_126915, 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: 30208
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1787 original size:28 final size:25

Alignment explanation


    Indices: 1756--1816  Score: 77
    Period size: 26  Copynumber: 2.3  Consensus size: 25

       1746 ATTTTAAAAA

                                        
       1756 TATATATTTATATTATATTTAATAATTT
          1 TATATATTTATATT-TA-TTAA-AATTT

                      *               
       1784 TATATAATTTTTATTTATTAAAATTT
          1 TATAT-ATTTATATTTATTAAAATTT

                   
       1810 TATATAT
          1 TATATAT

       1817 GATCACCTTA


Statistics
Matches: 31,  Mismatches: 1, Indels: 5
        0.84            0.03        0.14

Matches are distributed among these distances:
  25    2  0.06
  26   10  0.32
  27    4  0.13
  28    7  0.23
  29    8  0.26

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (25 bp):   
TATATATTTATATTTATTAAAATTT

Found at i:8687 original size:6 final size:6

Alignment explanation


    Indices: 8669--8700  Score: 55
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       8659 GCTGAAAGGT

                                                 
       8669 TAGCAC TTAGCAC TAGCAC TAGCAC TAGCAC T
          1 TAGCAC -TAGCAC TAGCAC TAGCAC TAGCAC T

       8701 GGACTTGCTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   19  0.76
   7    6  0.24

ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22


Consensus pattern (6 bp):   
TAGCAC

Found at i:15099 original size:14 final size:14

Alignment explanation


    Indices: 15080--15111  Score: 64
    Period size: 14  Copynumber: 2.3  Consensus size: 14

      15070 CAAAAGAAAA

                          
      15080 TGAAGAAATTTGAG
          1 TGAAGAAATTTGAG

                          
      15094 TGAAGAAATTTGAG
          1 TGAAGAAATTTGAG

                
      15108 TGAA
          1 TGAA

      15112 TGTTCTGTGT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28


Consensus pattern (14 bp):   
TGAAGAAATTTGAG

Found at i:15729 original size:31 final size:31

Alignment explanation


    Indices: 15688--15822  Score: 120
    Period size: 31  Copynumber: 4.5  Consensus size: 31

      15678 ACCCCAAAAA

                *       *             *     
      15688 TTTAAGTACCAACTTA-AAAAAAAGTGTCAAG
          1 TTTAGGTACCAAATTAGAAAAAAA-TATCAAG

                             *             
      15719 TTTAGGTACCAAATTAGGAAAAAATATCAAG
          1 TTTAGGTACCAAATTAGAAAAAAATATCAAG

                            *  *            
      15750 TTT-GAGTACCAAATTGGACAAAAA-A--AAG
          1 TTTAG-GTACCAAATTAGAAAAAAATATCAAG

                                    *      *
      15778 TTTAGGTACCAAATTA-AGAAAAATTATCAAA
          1 TTTAGGTACCAAATTAGA-AAAAAATATCAAG

              *           
      15809 TTCAGGTACCAAAT
          1 TTTAGGTACCAAAT

      15823 ATTATATTAA


Statistics
Matches: 85,  Mismatches: 12, Indels: 14
        0.77            0.11        0.13

Matches are distributed among these distances:
  27    1  0.01
  28   20  0.24
  29    2  0.02
  30    2  0.02
  31   54  0.64
  32    6  0.07

ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26


Consensus pattern (31 bp):   
TTTAGGTACCAAATTAGAAAAAAATATCAAG

Found at i:22837 original size:15 final size:15

Alignment explanation


    Indices: 22816--22858  Score: 52
    Period size: 14  Copynumber: 2.9  Consensus size: 15

      22806 TTCAGTTTGT

                           
      22816 ATTTTAATTATTTAC
          1 ATTTTAATTATTTAC

            *      *       
      22831 GTTTTAAATA-TTAC
          1 ATTTTAATTATTTAC

                  *       
      22845 ATTTTAGTTATTTA
          1 ATTTTAATTATTTA

      22859 TATTATCGTG


Statistics
Matches: 22,  Mismatches: 5, Indels: 2
        0.76            0.17        0.07

Matches are distributed among these distances:
  14   11  0.50
  15   11  0.50

ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58


Consensus pattern (15 bp):   
ATTTTAATTATTTAC

Found at i:30177 original size:2 final size:2

Alignment explanation


    Indices: 30170--30208  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      30160 TTTACTTTAT

                                                                      
      30170 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.