Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009974.1 Kokia drynarioides strain JFW-HI SEQ_124724, 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: 1751
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29


Found at i:272 original size:43 final size:43

Alignment explanation


    Indices: 191--275  Score: 118
    Period size: 43  Copynumber: 2.0  Consensus size: 43

        181 ATTAACATGT

                                  *        *           
        191 TAAATTATATTACTTGACTCATGTTAATATGGTTACATGTTAC
          1 TAAATTATATTACTTGACTCATATTAATATGCTTACATGTTAC

                           *    *                      
        234 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
          1 TAAATTATATTACTTGACTCATATTAATATGCTT-ACATGTTA

        276 TTAATTGTGC


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

Matches are distributed among these distances:
  42    2  0.05
  43   35  0.95

ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47


Consensus pattern (43 bp):   
TAAATTATATTACTTGACTCATATTAATATGCTTACATGTTAC

Found at i:978 original size:45 final size:45

Alignment explanation


    Indices: 843--979  Score: 166
    Period size: 45  Copynumber: 3.0  Consensus size: 45

        833 GCATAGCTCA

                  *           *                   *      
        843 TCAAGCTAAGGATATCAGTCTCAATTTGACGAGCCACCACAATAC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC

                                                         
        888 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC

                 **        *  *  * *         *  *   *    
        933 TCAAGGGAAGGATATTAGGCTGAGTTTGACGAGTCATCGCGATAC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC

              
        978 TC
          1 TC

        980 TATTCCTCCC


Statistics
Matches: 80,  Mismatches: 12, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  45   80  1.00

ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC

Found at i:1002 original size:21 final size:21

Alignment explanation


    Indices: 976--1016  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        966 TCATCGCGAT

                  *              
        976 ACTCTATTCCTCCCGGGCAAG
          1 ACTCTACTCCTCCCGGGCAAG

                         *      
        997 ACTCTACTCCTCCGGGGCAA
          1 ACTCTACTCCTCCCGGGCAA

       1017 ATGGACCCTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22


Consensus pattern (21 bp):   
ACTCTACTCCTCCCGGGCAAG
Done.