Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010274.1 Kokia drynarioides strain JFW-HI SEQ_125118, 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: 1975
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30


Found at i:846 original size:43 final size:43

Alignment explanation


    Indices: 764--848  Score: 109
    Period size: 43  Copynumber: 2.0  Consensus size: 43

        754 ATTAACATGT

                             *    *        *           
        764 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
          1 TAAATTATATTACTTGAATCGTATTAATATGCTTGCATGTTAC

                           *    *                      
        807 TAAATTATATTACTTTAATCTTATTAATAT-CTTGACATGTTA
          1 TAAATTATATTACTTGAATCGTATTAATATGCTTG-CATGTTA

        849 TTAATTGTGC


Statistics
Matches: 36,  Mismatches: 5, Indels: 2
        0.84            0.12        0.05

Matches are distributed among these distances:
  42    3  0.08
  43   33  0.92

ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47


Consensus pattern (43 bp):   
TAAATTATATTACTTGAATCGTATTAATATGCTTGCATGTTAC

Found at i:1479 original size:45 final size:45

Alignment explanation


    Indices: 1415--1540  Score: 189
    Period size: 45  Copynumber: 2.8  Consensus size: 45

       1405 GCATAGCTCA

                                             *           
       1415 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGTCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC

                                               *         
       1460 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCTCCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC

                 **           *  * *            
       1505 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCA
          1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCA

       1541 TCGAGATACT


Statistics
Matches: 73,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  45   73  1.00

ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC

Found at i:1572 original size:21 final size:21

Alignment explanation


    Indices: 1546--1588  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1536 AGCCATCGAG

                    *            
       1546 ATACTCTATTCCTCCCGGGCA
          1 ATACTCTACTCCTCCCGGGCA

                       *   *     
       1567 ATACTCTACTCTTCCGGGGCA
          1 ATACTCTACTCCTCCCGGGCA

             
       1588 A
          1 A

       1589 ATGGACCCTA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28


Consensus pattern (21 bp):   
ATACTCTACTCCTCCCGGGCA
Done.