Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002999.1 Kokia drynarioides strain JFW-HI SEQ_115492, 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: 1974
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33


Found at i:64 original size:42 final size:42

Alignment explanation


    Indices: 1--260  Score: 371
    Period size: 42  Copynumber: 6.1  Consensus size: 42

                                      *              *
          1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGA
          1 AATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGC

                            *                    *     
         43 AATGAAAAGTAAATGGGCCTCCACACTTGGGCCCTCTGAATGC
          1 AATGAAAAGTAAATGGACCTCCACACTTGGG-CCTCTAAATGC

            *                    *                    
         86 GATGAAAAGTAAATGGACCTCTACACTTGGGCCTCTAAATGC
          1 AATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGC

                                      *               
        128 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
          1 AATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGC

                            *        *    *     *       
        170 AATGAAAAAGTAAAT-AAGCCTCCATACTTAGGCCTTTAAATGC
          1 AATG-AAAAGTAAATGGA-CCTCCACACTTGGGCCTCTAAATGC

                                                       
        213 AATGAAAAGTAAATGGACCGT-CACACTTGGGCCTCTAAATGC
          1 AATGAAAAGTAAATGGACC-TCCACACTTGGGCCTCTAAATGC

                  
        255 AATGAA
          1 AATGAA

        261 TGTTTTCCTT


Statistics
Matches: 193,  Mismatches: 20, Indels: 10
        0.87            0.09        0.04

Matches are distributed among these distances:
  42  119  0.62
  43   74  0.38

ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22


Consensus pattern (42 bp):   
AATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGC

Found at i:149 original size:85 final size:84

Alignment explanation


    Indices: 1--260  Score: 371
    Period size: 85  Copynumber: 3.1  Consensus size: 84

                                      *              *                *      
          1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGAAATGAAAAGTAAATGGGCCTCCA
          1 AATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCA

                          *     
         66 CACTTGGGCCCTCTGAATGC
         66 CACTTGGG-CCTCTAAATGC

            *                    *                                           
         86 GATGAAAAGTAAATGGACCTCTACACTTGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCA
          1 AATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCA

               *               
        151 CACCTGGGCCTCTAAATGC
         66 CACTTGGGCCTCTAAATGC

                            *        *    *     *                            
        170 AATGAAAAAGTAAAT-AAGCCTCCATACTTAGGCCTTTAAATGCAATGAAAAGTAAATGGACCGT
          1 AATG-AAAAGTAAATGGA-CCTCCACACTTGGGCCTCTAAATGCAATGAAAAGTAAATGGACC-T

                                  
        234 -CACACTTGGGCCTCTAAATGC
         63 CCACACTTGGGCCTCTAAATGC

                  
        255 AATGAA
          1 AATGAA

        261 TGTTTTCCTT


Statistics
Matches: 158,  Mismatches: 14, Indels: 7
        0.88            0.08        0.04

Matches are distributed among these distances:
  84   16  0.10
  85  141  0.89
  86    1  0.01

ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22


Consensus pattern (84 bp):   
AATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCA
CACTTGGGCCTCTAAATGC

Found at i:227 original size:127 final size:127

Alignment explanation


    Indices: 1--260  Score: 416
    Period size: 127  Copynumber: 2.0  Consensus size: 127

                                                                    **       
          1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGAAATGAAAAGTAAATGGGCCTCCA
          1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGAAATGAAAAGTAAATAAGCCTCCA

                 *        *     *                                          
         66 CACTTGGGCCCTCTGAATGCGATGAAAAGTAAATGGACC-TCTACACTTGGGCCTCTAAATGC
         66 CACTTAGGCCCTCTAAATGCAATGAAAAGTAAATGGACCGTC-ACACTTGGGCCTCTAAATGC

                                                     *                       
        128 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAAGTAAATAAGCCTCC
          1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGAAATG-AAAAGTAAATAAGCCTCC

             *           *                                                 
        193 ATACTTAGG-CCTTTAAATGCAATGAAAAGTAAATGGACCGTCACACTTGGGCCTCTAAATGC
         65 ACACTTAGGCCCTCTAAATGCAATGAAAAGTAAATGGACCGTCACACTTGGGCCTCTAAATGC

                  
        255 AATGAA
          1 AATGAA

        261 TGTTTTCCTT


Statistics
Matches: 123,  Mismatches: 8, Indels: 4
        0.91            0.06        0.03

Matches are distributed among these distances:
 127   98  0.80
 128   25  0.20

ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22


Consensus pattern (127 bp):   
AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGAAATGAAAAGTAAATAAGCCTCCA
CACTTAGGCCCTCTAAATGCAATGAAAAGTAAATGGACCGTCACACTTGGGCCTCTAAATGC
Done.