Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009945.1 Kokia drynarioides strain JFW-HI SEQ_124688, 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: 8912
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:1521 original size:6 final size:6

Alignment explanation


    Indices: 1510--1538  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       1500 TGATCAAAAT

                                             
       1510 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
          1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA

       1539 TTGGGATTGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17


Consensus pattern (6 bp):   
TGAAAG

Found at i:1549 original size:18 final size:18

Alignment explanation


    Indices: 1506--1554  Score: 62
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       1496 TTTGTGATCA

                              
       1506 AAATTGAAAGTGAAAGTG
          1 AAATTGAAAGTGAAAGTG

               *           *  
       1524 AAAGTGAAAGTGAAATTG
          1 AAATTGAAAGTGAAAGTG

            **           
       1542 GGATTGAAAGTGA
          1 AAATTGAAAGTGA

       1555 TATGAATTGT


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  18   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22


Consensus pattern (18 bp):   
AAATTGAAAGTGAAAGTG

Found at i:1749 original size:37 final size:38

Alignment explanation


    Indices: 1654--1760  Score: 99
    Period size: 37  Copynumber: 2.8  Consensus size: 38

       1644 CTTCGACGTT

                                    ** *             
       1654 GAGTCGATGAGACACTAGGTGTCATTATTTTACTTTGGATA
          1 GAGTCGATGAGACACT-GG-GT-ACCACTTTACTTTGGATA

              *        **                      *  
       1695 GATTCGATGAGGTACTGGGTACCACTTTACTTTGGCTA
          1 GAGTCGATGAGACACTGGGTACCACTTTACTTTGGATA

                                **       
       1733 G-GTCGATGAGACACTGGGTGTCACTTTA
          1 GAGTCGATGAGACACTGGGTACCACTTTA

       1761 TTGCTTCGAA


Statistics
Matches: 54,  Mismatches: 12, Indels: 4
        0.77            0.17        0.06

Matches are distributed among these distances:
  37   22  0.41
  38   15  0.28
  39    2  0.04
  40    2  0.04
  41   13  0.24

ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34


Consensus pattern (38 bp):   
GAGTCGATGAGACACTGGGTACCACTTTACTTTGGATA

Found at i:3843 original size:18 final size:18

Alignment explanation


    Indices: 3820--3880  Score: 61
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       3810 TACAAAAGAA

                              
       3820 AAAATTCAAAATAATTTT
          1 AAAATTCAAAATAATTTT

                   *           *
       3838 AAAATTCTAAAT-ATCTATA
          1 AAAATTCAAAATAAT-T-TT

                                
       3857 AAAATTCAAATTATAATTTT
          1 AAAATTCAAA--ATAATTTT

                
       3877 AAAA
          1 AAAA

       3881 AAATTATAAA


Statistics
Matches: 34,  Mismatches: 4, Indels: 8
        0.74            0.09        0.17

Matches are distributed among these distances:
  17    2  0.06
  18   12  0.35
  19   10  0.29
  20    5  0.15
  21    3  0.09
  22    2  0.06

ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38


Consensus pattern (18 bp):   
AAAATTCAAAATAATTTT

Found at i:3901 original size:21 final size:20

Alignment explanation


    Indices: 3871--3917  Score: 60
    Period size: 21  Copynumber: 2.3  Consensus size: 20

       3861 TTCAAATTAT

                                 
       3871 AATTTTAAAA-AAATTATAAA
          1 AATTTTAAAATAAATT-TAAA

                          *      
       3891 AATTTTAAAAATAAGTTTAAA
          1 AATTTT-AAAATAAATTTAAA

                  
       3912 AATTTT
          1 AATTTT

       3918 CTTAAATAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  20    6  0.25
  21   14  0.58
  22    4  0.17

ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40


Consensus pattern (20 bp):   
AATTTTAAAATAAATTTAAA
Done.