Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004480.1 Kokia drynarioides strain JFW-HI SEQ_117902, 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: 4243
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30


Found at i:1779 original size:43 final size:43

Alignment explanation


    Indices: 1718--1803  Score: 163
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       1708 GAAGAGGAGG

                               *                       
       1718 ATGAAGAGGCATTAGATGATGATGATTCTTATCGTCTTGATTT
          1 ATGAAGAGGCATTAGATGACGATGATTCTTATCGTCTTGATTT

                                                       
       1761 ATGAAGAGGCATTAGATGACGATGATTCTTATCGTCTTGATTT
          1 ATGAAGAGGCATTAGATGACGATGATTCTTATCGTCTTGATTT

       1804 TGCGGGATCA


Statistics
Matches: 42,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   42  1.00

ACGTcount: A:0.28, C:0.10, G:0.23, T:0.38


Consensus pattern (43 bp):   
ATGAAGAGGCATTAGATGACGATGATTCTTATCGTCTTGATTT

Found at i:1896 original size:45 final size:45

Alignment explanation


    Indices: 1832--1954  Score: 174
    Period size: 45  Copynumber: 2.7  Consensus size: 45

       1822 GCATAGCTCA

                    *                              *     
       1832 TCAAGCCATGGATATCAGCCTCAGTTTGACGAGCCACCGTAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

                                   *     *               
       1877 TCAAGCCAAGGATATCAGCCTCAATTTGATGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

                 **           *  *           
       1922 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAG
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAG

       1955 TCATCACGAT


Statistics
Matches: 68,  Mismatches: 10, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  45   68  1.00

ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

Found at i:1967 original size:45 final size:43

Alignment explanation


    Indices: 1832--1968  Score: 148
    Period size: 45  Copynumber: 3.0  Consensus size: 43

       1822 GCATAGCTCA

                    *                                    
       1832 TCAAGCCATGGATATCAGCCTCAGTTTGACGAGCCACCGTAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCG--ATAC

                                   *     *               
       1877 TCAAGCCAAGGATATCAGCCTCAATTTGATGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCG--ATAC

                 **           *  *           *           
       1922 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGTCATCACGATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCA-C-CGATAC

              
       1967 TC
          1 TC

       1969 TATTCCTCCC


Statistics
Matches: 79,  Mismatches: 11, Indels: 4
        0.84            0.12        0.04

Matches are distributed among these distances:
  45   76  0.96
  46    1  0.01
  47    2  0.03

ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22


Consensus pattern (43 bp):   
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGATAC

Found at i:1991 original size:21 final size:21

Alignment explanation


    Indices: 1965--2005  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1955 TCATCACGAT

                  *              
       1965 ACTCTATTCCTCCCGGGCAAG
          1 ACTCTACTCCTCCCGGGCAAG

                         *      
       1986 ACTCTACTCCTCCGGGGCAA
          1 ACTCTACTCCTCCCGGGCAA

       2006 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.