Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015262.1 Kokia drynarioides strain JFW-HI SEQ_130307, 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: 411148
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33

Warning! 200 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:394866 original size:27 final size:26

Alignment explanation


    Indices: 394828--394887  Score: 77
    Period size: 27  Copynumber: 2.2  Consensus size: 26

     394818 AACCAAACAC

                             *          
     394828 GGTTTGTATGAG-GTGGTTAGTTGAAAG
          1 GGTTTGTATGAGAG-GGAT-GTTGAAAG

                                       
     394855 GGTTTGTATGAGACGGGATGTTGAAAG
          1 GGTTTGTATGAGA-GGGATGTTGAAAG

                  
     394882 GGTTTG
          1 GGTTTG

     394888 CAATCGATGC


Statistics
Matches: 30,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  27   26  0.87
  28    3  0.10
  29    1  0.03

ACGTcount: A:0.22, C:0.02, G:0.42, T:0.35


Consensus pattern (26 bp):   
GGTTTGTATGAGAGGGATGTTGAAAG

Found at i:395891 original size:15 final size:15

Alignment explanation


    Indices: 395873--395910  Score: 51
    Period size: 15  Copynumber: 2.5  Consensus size: 15

     395863 ACATGAATAG

                            
     395873 TACGAGCATGGATA-T
          1 TACGAGCATGGA-AGT

                *          
     395888 TACGTGCATGGAAGT
          1 TACGAGCATGGAAGT

                    
     395903 TACGAGCA
          1 TACGAGCA

     395911 GTAATGCTCT


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

Matches are distributed among these distances:
  14    1  0.05
  15   19  0.95

ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24


Consensus pattern (15 bp):   
TACGAGCATGGAAGT

Found at i:395938 original size:15 final size:15

Alignment explanation


    Indices: 395915--395948  Score: 59
    Period size: 15  Copynumber: 2.3  Consensus size: 15

     395905 CGAGCAGTAA

                *          
     395915 TGCTCTGAACACTAG
          1 TGCTATGAACACTAG

                           
     395930 TGCTATGAACACTAG
          1 TGCTATGAACACTAG

                
     395945 TGCT
          1 TGCT

     395949 GCGAGCACTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29


Consensus pattern (15 bp):   
TGCTATGAACACTAG

Found at i:395957 original size:15 final size:15

Alignment explanation


    Indices: 395924--395973  Score: 55
    Period size: 15  Copynumber: 3.3  Consensus size: 15

     395914 ATGCTCTGAA

                      **  *
     395924 CACTAGTGCTATGAA
          1 CACTAGTGCTGCGAG

                           
     395939 CACTAGTGCTGCGAG
          1 CACTAGTGCTGCGAG

                 * *       
     395954 CACTACTACTGCGAG
          1 CACTAGTGCTGCGAG

                 
     395969 CACTA
          1 CACTA

     395974 AAGTTACAAA


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  15   30  1.00

ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22


Consensus pattern (15 bp):   
CACTAGTGCTGCGAG

Done.