Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012905.1 Kokia drynarioides strain JFW-HI SEQ_127919, 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: 5355
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:1275 original size:43 final size:43

Alignment explanation


    Indices: 1193--1277  Score: 118
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       1183 ACTAACATGT

                                  *        *           
       1193 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
          1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC

                           *    *                      
       1236 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
          1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA

       1278 TTAATTGTGC


Statistics
Matches: 37,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  42    3  0.08
  43   34  0.92

ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47


Consensus pattern (43 bp):   
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC

Found at i:1980 original size:45 final size:45

Alignment explanation


    Indices: 1845--1981  Score: 175
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       1835 GCATAGCTCA

                             *                   *       
       1845 TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACTGCAATAC

                                   *         *    *      
       1890 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGTCACTACAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACTGCAATAC

                 **           *  *              *   *    
       1935 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCATTGCGATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACTGCAATAC

              
       1980 TC
          1 TC

       1982 TATTTCTCTC


Statistics
Matches: 78,  Mismatches: 14, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  45   78  1.00

ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACTGCAATAC

Found at i:2264 original size:14 final size:14

Alignment explanation


    Indices: 2247--2286  Score: 55
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       2237 CATTAAACCT

                *         
       2247 TAAAACCTAAATTA
          1 TAAACCCTAAATTA

                           
       2261 TAAACCCTAAACTTA
          1 TAAACCCTAAA-TTA

                        
       2276 -AAACCCTAAAT
          1 TAAACCCTAAAT

       2287 CGTAAAGTTA


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

Matches are distributed among these distances:
  13    1  0.04
  14   20  0.83
  15    3  0.12

ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25


Consensus pattern (14 bp):   
TAAACCCTAAATTA
Done.