Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014384.1 Kokia drynarioides strain JFW-HI SEQ_129422, 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, 993

Length: 1655
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24


Found at i:949 original size:72 final size:72

Alignment explanation


    Indices: 832--995  Score: 328
    Period size: 72  Copynumber: 2.3  Consensus size: 72

        822 CGGTAATCTT

                                                                             
        832 CCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTCGACATGAGCAAATCTTCGAACC
          1 CCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTCGACATGAGCAAATCTTCGAACC

                   
        897 ACAGCTC
         66 ACAGCTC

                                                                             
        904 CCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTCGACATGAGCAAATCTTCGAACC
          1 CCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTCGACATGAGCAAATCTTCGAACC

                   
        969 ACAGCTC
         66 ACAGCTC

                                
        976 CCTGATGAGATACTGAGAAG
          1 CCTGATGAGATACTGAGAAG

        996 CGTGTCGAAG


Statistics
Matches: 92,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  72   92  1.00

ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16


Consensus pattern (72 bp):   
CCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTCGACATGAGCAAATCTTCGAACC
ACAGCTC

Found at i:969 original size:34 final size:34

Alignment explanation


    Indices: 859--969  Score: 82
    Period size: 34  Copynumber: 3.1  Consensus size: 34

        849 AAGAAGACCA

                                              
        859 AACCAAACCCATGCTCGACATGAGCAAATCTTCG
          1 AACCAAACCCATGCTCGACATGAGCAAATCTTCG

                   *    *  *  *  *      *     *    *
        893 AACCACAGCTCCCTGATGAGATACTGAGAAGAAGAC--CA
          1 AACCA-AAC-CCATGCT-CGACA-TGAGCA-AA-TCTTCG

                                              
        931 AACCAAACCCATGCTCGACATGAGCAAATCTTCG
          1 AACCAAACCCATGCTCGACATGAGCAAATCTTCG

                 
        965 AACCA
          1 AACCA

        970 CAGCTCCCTG


Statistics
Matches: 53,  Mismatches: 16, Indels: 16
        0.62            0.19        0.19

Matches are distributed among these distances:
  32    1  0.02
  33    2  0.04
  34   16  0.30
  35    5  0.09
  36   10  0.19
  37    5  0.09
  38   11  0.21
  39    2  0.04
  40    1  0.02

ACGTcount: A:0.38, C:0.31, G:0.16, T:0.15


Consensus pattern (34 bp):   
AACCAAACCCATGCTCGACATGAGCAAATCTTCG

Found at i:1594 original size:17 final size:17

Alignment explanation


    Indices: 1567--1640  Score: 94
    Period size: 17  Copynumber: 4.4  Consensus size: 17

       1557 TTGGAAATTG

                *            
       1567 AATTCATTTTAAATTTA
          1 AATTTATTTTAAATTTA

             *               
       1584 AGTTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

             *       *       
       1601 AGTTTATTTGAAATTTA
          1 AATTTATTTTAAATTTA

                    *    *   
       1618 AATTTATTATAAAATTA
          1 AATTTATTTTAAATTTA

                  
       1635 AATTTA
          1 AATTTA

       1641 GAAAAGTCCA


Statistics
Matches: 50,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   50  1.00

ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53


Consensus pattern (17 bp):   
AATTTATTTTAAATTTA

Done.