Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015050.1 Kokia drynarioides strain JFW-HI SEQ_130094, 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: 33562
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33

Warning! 11 characters in sequence are not A, C, G, or T


Found at i:1893 original size:29 final size:29

Alignment explanation


    Indices: 1860--1919  Score: 102
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       1850 TATGTTTTAA

                                *        
       1860 TGTGCAATTTTATACATGAATTTTTATTT
          1 TGTGCAATTTTATACATGAAATTTTATTT

                                     *   
       1889 TGTGCAATTTTATACATGAAATTTTGTTT
          1 TGTGCAATTTTATACATGAAATTTTATTT

              
       1918 TG
          1 TG

       1920 ATCCAATTCT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53


Consensus pattern (29 bp):   
TGTGCAATTTTATACATGAAATTTTATTT

Found at i:1927 original size:30 final size:29

Alignment explanation


    Indices: 1864--1927  Score: 92
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       1854 TTTTAATGTG

                            *           *
       1864 CAATTTTATACATGAATTTTTATTTTGTG
          1 CAATTTTATACATGAAATTTTATTTTGTC

                                 *        
       1893 CAATTTTATACATGAAATTTTGTTTTGATC
          1 CAATTTTATACATGAAATTTTATTTTG-TC

                 
       1923 CAATT
          1 CAATT

       1928 CTTGTAAATA


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  29   25  0.81
  30    6  0.19

ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52


Consensus pattern (29 bp):   
CAATTTTATACATGAAATTTTATTTTGTC

Found at i:10868 original size:32 final size:32

Alignment explanation


    Indices: 10830--10892  Score: 90
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      10820 CTTCACCCTG

                     *                      
      10830 CCCCTAAGTTGTATTTATGAATCGACCATTGC
          1 CCCCTAAGTCGTATTTATGAATCGACCATTGC

                            *  *     *     
      10862 CCCCTAAGTCGTATTTTTGGATCGATCATTG
          1 CCCCTAAGTCGTATTTATGAATCGACCATTG

      10893 TTGTTCACTA


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37


Consensus pattern (32 bp):   
CCCCTAAGTCGTATTTATGAATCGACCATTGC

Found at i:11349 original size:106 final size:106

Alignment explanation


    Indices: 11227--11441  Score: 421
    Period size: 106  Copynumber: 2.0  Consensus size: 106

      11217 AGCCTCCCCA

                                                                             
      11227 TGCTATTTGAGAGAGCTTATATACACGAGACAATAGAGATGCTCCTTATCAATTACAGGCCAAAT
          1 TGCTATTTGAGAGAGCTTATATACACGAGACAATAGAGATGCTCCTTATCAATTACAGGCCAAAT

                                                     
      11292 TTACAATCATAATGAAGCTTAAGTATACAAAACTTAGAACT
         66 TTACAATCATAATGAAGCTTAAGTATACAAAACTTAGAACT

                                                  *                          
      11333 TGCTATTTGAGAGAGCTTATATACACGAGACAATAGAGTTGCTCCTTATCAATTACAGGCCAAAT
          1 TGCTATTTGAGAGAGCTTATATACACGAGACAATAGAGATGCTCCTTATCAATTACAGGCCAAAT

                                                     
      11398 TTACAATCATAATGAAGCTTAAGTATACAAAACTTAGAACT
         66 TTACAATCATAATGAAGCTTAAGTATACAAAACTTAGAACT

               
      11439 TGC
          1 TGC

      11442 ACATCTTCCC


Statistics
Matches: 108,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 106  108  1.00

ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29


Consensus pattern (106 bp):   
TGCTATTTGAGAGAGCTTATATACACGAGACAATAGAGATGCTCCTTATCAATTACAGGCCAAAT
TTACAATCATAATGAAGCTTAAGTATACAAAACTTAGAACT
Done.