Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007263.1 Kokia drynarioides strain JFW-HI SEQ_121879, 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: 5991
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:72 original size:48 final size:48

Alignment explanation


    Indices: 1--106  Score: 185
    Period size: 48  Copynumber: 2.2  Consensus size: 48

                                                    *       
          1 ACGGTCGTTGCTCGTGCTCCTTCTCCTGTCGGTGCTGATGGCCCAAAT
          1 ACGGTCGTTGCTCGTGCTCCTTCTCCTGTCGGTGCTGATGACCCAAAT

                     *   *                                  
         49 ACGGTCGTTTCTCTTGCTCCTTCTCCTGTCGGTGCTGATGACCCAAAT
          1 ACGGTCGTTGCTCGTGCTCCTTCTCCTGTCGGTGCTGATGACCCAAAT

                      
         97 ACGGTCGTTG
          1 ACGGTCGTTG

        107 ATCCTCCCCC


Statistics
Matches: 54,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  48   54  1.00

ACGTcount: A:0.11, C:0.30, G:0.25, T:0.33


Consensus pattern (48 bp):   
ACGGTCGTTGCTCGTGCTCCTTCTCCTGTCGGTGCTGATGACCCAAAT

Found at i:1879 original size:3 final size:3

Alignment explanation


    Indices: 1866--1913  Score: 87
    Period size: 3  Copynumber: 15.7  Consensus size: 3

       1856 AATAACAATT

                                                                        
       1866 TAA TGAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

              
       1912 TA
          1 TA

       1914 CATCAACAGT


Statistics
Matches: 44,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   3   41  0.93
   4    3  0.07

ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33


Consensus pattern (3 bp):   
TAA

Found at i:4201 original size:30 final size:30

Alignment explanation


    Indices: 4165--4229  Score: 103
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       4155 TTTTATTTTA

                           *        *     
       4165 TTGTTAATTTTGTTATTATTTTAGCGGCAC
          1 TTGTTAATTTTGTTACTATTTTAGAGGCAC

                                         *
       4195 TTGTTAATTTTGTTACTATTTTAGAGGCAT
          1 TTGTTAATTTTGTTACTATTTTAGAGGCAC

                 
       4225 TTGTT
          1 TTGTT

       4230 TATTAAGTTA


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  30   32  1.00

ACGTcount: A:0.20, C:0.08, G:0.17, T:0.55


Consensus pattern (30 bp):   
TTGTTAATTTTGTTACTATTTTAGAGGCAC

Found at i:4240 original size:30 final size:30

Alignment explanation


    Indices: 4165--4240  Score: 80
    Period size: 30  Copynumber: 2.5  Consensus size: 30

       4155 TTTTATTTTA

                     **    *        *     
       4165 TTGTTAATTTTGTTATTATTTTAGCGGCAC
          1 TTGTTAATTAAGTTACTATTTTAGAGGCAC

                     **                  *
       4195 TTGTTAATTTTGTTACTATTTTAGAGGCAT
          1 TTGTTAATTAAGTTACTATTTTAGAGGCAC

                 *          
       4225 TTGTTTATTAAGTTAC
          1 TTGTTAATTAAGTTAC

       4241 ATCTATCTTA


Statistics
Matches: 40,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  30   40  1.00

ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54


Consensus pattern (30 bp):   
TTGTTAATTAAGTTACTATTTTAGAGGCAC
Done.