Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008976.1 Kokia drynarioides strain JFW-HI SEQ_123673, 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: 3280
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28


Found at i:191 original size:10 final size:10

Alignment explanation


    Indices: 176--217  Score: 50
    Period size: 10  Copynumber: 4.2  Consensus size: 10

        166 TCATATAAAT

                      
        176 AAAGTAAAGC
          1 AAAGTAAAGC

                      
        186 AAAGTAAAGC
          1 AAAGTAAAGC

                *    *
        196 AAAGCAAAGT
          1 AAAGTAAAGC

                       
        206 AAA-TCAAAGC
          1 AAAGT-AAAGC

              
        216 AA
          1 AA

        218 TATAAAACAA


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  10   27  1.00

ACGTcount: A:0.62, C:0.12, G:0.17, T:0.10


Consensus pattern (10 bp):   
AAAGTAAAGC

Found at i:199 original size:15 final size:15

Alignment explanation


    Indices: 175--217  Score: 68
    Period size: 15  Copynumber: 2.9  Consensus size: 15

        165 ATCATATAAA

                 *         
        175 TAAAGTAAAGCAAAG
          1 TAAAGCAAAGCAAAG

                           
        190 TAAAGCAAAGCAAAG
          1 TAAAGCAAAGCAAAG

                *        
        205 TAAATCAAAGCAA
          1 TAAAGCAAAGCAA

        218 TATAAAACAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   26  1.00

ACGTcount: A:0.60, C:0.12, G:0.16, T:0.12


Consensus pattern (15 bp):   
TAAAGCAAAGCAAAG

Found at i:223 original size:15 final size:15

Alignment explanation


    Indices: 181--229  Score: 64
    Period size: 15  Copynumber: 3.3  Consensus size: 15

        171 TAAATAAAGT

                         * 
        181 AAAGCAAAGTAAAGC
          1 AAAGCAAAGTAAAAC

                         * 
        196 AAAGCAAAGTAAATC
          1 AAAGCAAAGTAAAAC

                            
        211 AAAGCAATA-TAAAAC
          1 AAAGCAA-AGTAAAAC

                
        226 AAAG
          1 AAAG

        230 ATGATATAAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  15   30  0.97
  16    1  0.03

ACGTcount: A:0.63, C:0.12, G:0.14, T:0.10


Consensus pattern (15 bp):   
AAAGCAAAGTAAAAC

Found at i:3105 original size:15 final size:15

Alignment explanation


    Indices: 3073--3106  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       3063 ATTGTTTTGA

                         * 
       3073 TTTAATTTGCTTTGC
          1 TTTAATTTGCTTTAC

                *          
       3088 TTTACTTTGCTTTAC
          1 TTTAATTTGCTTTAC

                
       3103 TTTA
          1 TTTA

       3107 TTTATATGAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.15, C:0.15, G:0.09, T:0.62


Consensus pattern (15 bp):   
TTTAATTTGCTTTAC
Done.