Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011100.1 Kokia drynarioides strain JFW-HI SEQ_126073, 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: 13730
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:943 original size:21 final size:21

Alignment explanation


    Indices: 919--986  Score: 61
    Period size: 21  Copynumber: 3.3  Consensus size: 21

        909 TTCATTAGAT

                                 
        919 AAGTTAGTATATCATACAATG
          1 AAGTTAGTATATCATACAATG

                   * *    *        
        940 AAGTTA-CACAGTCTTA-ATAT-
          1 AAGTTAGTATA-TCATACA-ATG

                               * 
        960 AAGTTAGTATATCATACAACG
          1 AAGTTAGTATATCATACAATG

                  
        981 AAGTTA
          1 AAGTTA

        987 CACAGTCTTA


Statistics
Matches: 35,  Mismatches: 7, Indels: 10
        0.67            0.13        0.19

Matches are distributed among these distances:
  20   14  0.40
  21   21  0.60

ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32


Consensus pattern (21 bp):   
AAGTTAGTATATCATACAATG

Found at i:974 original size:41 final size:41

Alignment explanation


    Indices: 917--999  Score: 157
    Period size: 41  Copynumber: 2.0  Consensus size: 41

        907 ATTTCATTAG

                                 *                   
        917 ATAAGTTAGTATATCATACAATGAAGTTACACAGTCTTAAT
          1 ATAAGTTAGTATATCATACAACGAAGTTACACAGTCTTAAT

                                                     
        958 ATAAGTTAGTATATCATACAACGAAGTTACACAGTCTTAAT
          1 ATAAGTTAGTATATCATACAACGAAGTTACACAGTCTTAAT

             
        999 A
          1 A

       1000 AACATAATTA


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  41   41  1.00

ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33


Consensus pattern (41 bp):   
ATAAGTTAGTATATCATACAACGAAGTTACACAGTCTTAAT

Found at i:8303 original size:19 final size:19

Alignment explanation


    Indices: 8279--8317  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       8269 AAAGTTGGGT

                               
       8279 GTCAATATTTGATGAAATA
          1 GTCAATATTTGATGAAATA

                               
       8298 GTCAATATTTGATGAAATA
          1 GTCAATATTTGATGAAATA

             
       8317 G
          1 G

       8318 AAAGTGAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36


Consensus pattern (19 bp):   
GTCAATATTTGATGAAATA

Found at i:8662 original size:2 final size:2

Alignment explanation


    Indices: 8614--8652  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       8604 TCTAGTCCAA

                                                                      
       8614 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C

       8653 GTATTCTCTC


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


Consensus pattern (2 bp):   
CT

Found at i:8949 original size:2 final size:2

Alignment explanation


    Indices: 8903--8939  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       8893 TCTATTCCAA

                                          *                        
       8903 CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT C
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C

       8940 GTATTCTCTC


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49


Consensus pattern (2 bp):   
CT
Done.