Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007371.1 Kokia drynarioides strain JFW-HI SEQ_121987, 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: 18440
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:34 original size:18 final size:18

Alignment explanation


    Indices: 2--40  Score: 53
    Period size: 17  Copynumber: 2.2  Consensus size: 18

          1 T

                      *        
          2 TTTATAATATTTAAAAATA
          1 TTTATAATATAT-AAAATA

                              
         21 TTTA-AATATATAAAATA
          1 TTTATAATATATAAAATA

               
         38 TTT
          1 TTT

         41 TTCAACATTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17    9  0.47
  18    6  0.32
  19    4  0.21

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


Consensus pattern (18 bp):   
TTTATAATATATAAAATA

Found at i:167 original size:15 final size:16

Alignment explanation


    Indices: 147--179  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

        137 CTAAAATAAA

                         *  
        147 AAAATTTT-GATTTAT
          1 AAAATTTTAGATTAAT

                            
        162 AAAATTTTAGATTAAT
          1 AAAATTTTAGATTAAT

              
        178 AA
          1 AA

        180 TAATAAAAAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45


Consensus pattern (16 bp):   
AAAATTTTAGATTAAT

Found at i:1625 original size:24 final size:23

Alignment explanation


    Indices: 1598--1661  Score: 74
    Period size: 24  Copynumber: 2.7  Consensus size: 23

       1588 TCATTAACAT

                                    
       1598 TGTTCGTGAACATGTTCACTTATA
          1 TGTTCGTGAACATGTTCACTTA-A

                 *        *  **    
       1622 TGTTCATGAACATGCTCGTTTAA
          1 TGTTCGTGAACATGTTCACTTAA

                *            
       1645 TGTTTGTGAACATGTTC
          1 TGTTCGTGAACATGTTC

       1662 GATTAAGTTA


Statistics
Matches: 33,  Mismatches: 7, Indels: 1
        0.80            0.17        0.02

Matches are distributed among these distances:
  23   15  0.45
  24   18  0.55

ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42


Consensus pattern (23 bp):   
TGTTCGTGAACATGTTCACTTAA

Found at i:1695 original size:23 final size:23

Alignment explanation


    Indices: 1651--1696  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1641 TTAATGTTTG

                          *  *     
       1651 TGAACATGTTCGATTAAGTTAAA
          1 TGAACATGTTCGATGAAATTAAA

                                    
       1674 TGAACATGTTCG-TGAACATTAAA
          1 TGAACATGTTCGATGAA-ATTAAA

       1697 CAAACGAACA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  22    3  0.15
  23   17  0.85

ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33


Consensus pattern (23 bp):   
TGAACATGTTCGATGAAATTAAA

Found at i:10991 original size:29 final size:30

Alignment explanation


    Indices: 10928--10992  Score: 71
    Period size: 31  Copynumber: 2.2  Consensus size: 30

      10918 AAAATTATAG

                                        * *
      10928 ATGAATTTTGATTTGATATGTAATTTGATAT
          1 ATGAATTTTGATTTGA-ATGTAATTTGACAC

                            *              
      10959 ATGAATTTTGATTTG-GTGTAATTAT-ACAC
          1 ATGAATTTTGATTTGAATGTAATT-TGACAC

                 
      10988 ATGAA
          1 ATGAA

      10993 AATTTAGTTA


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  29   14  0.47
  30    1  0.03
  31   15  0.50

ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46


Consensus pattern (30 bp):   
ATGAATTTTGATTTGAATGTAATTTGACAC

Found at i:11601 original size:2 final size:2

Alignment explanation


    Indices: 11594--11624  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      11584 ATAAAAAGAC

                                                          
      11594 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

      11625 CAGCTGGTTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00


Consensus pattern (2 bp):   
AG

Done.