Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005317.1 Kokia drynarioides strain JFW-HI SEQ_119251, 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: 28442
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.31

Warning! 333 characters in sequence are not A, C, G, or T


Found at i:8403 original size:65 final size:65

Alignment explanation


    Indices: 8299--8440  Score: 194
    Period size: 65  Copynumber: 2.2  Consensus size: 65

       8289 ATGCAAATTT

                          *       **    *           *     **                 
       8299 ACATCCAAATTTGCTAATAACTTTGTTTGAAGAAAGAAAGTACACTGGATGAGGATTTTGGAGTC
          1 ACATCCAAATTTGCAAATAACTCCGTTTCAAGAAAGAAAGCACACTAAATGAGGATTTTGGAGTC

                                            *                 *              
       8364 ACATCCAAATTTGCAAATAACTCCGTTTCAAGGAAGAAAGCACACTAAATTAGGATTTTGGAGTC
          1 ACATCCAAATTTGCAAATAACTCCGTTTCAAGAAAGAAAGCACACTAAATGAGGATTTTGGAGTC

                *       
       8429 ACATGCAAATTT
          1 ACATCCAAATTT

       8441 ACATCCAAAT


Statistics
Matches: 67,  Mismatches: 10, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  65   67  1.00

ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29


Consensus pattern (65 bp):   
ACATCCAAATTTGCAAATAACTCCGTTTCAAGAAAGAAAGCACACTAAATGAGGATTTTGGAGTC

Found at i:8497 original size:78 final size:77

Alignment explanation


    Indices: 8364--8518  Score: 247
    Period size: 78  Copynumber: 2.0  Consensus size: 77

       8354 TTTTGGAGTC

                                                   *     *    *              
       8364 ACATCCAAATTTGCAAATAACTCCGTTTCAAGGAAGAAAGCACACTAAATTAGGATTTTGGAGTC
          1 ACATCCAAATTTGCAAATAACTCCGTTTCAAGGAAGAAAACACACCAAATGAGGATTTTGGAGTC

                        
       8429 ACATGCAAATTT
         66 ACATGCAAATTT

                                         *                  *                
       8441 ACATCCAAATTTGCCAAATAACTCCGTTTGAAGGAAGAAAACACACCAGATGAGGATTTTGGAGT
          1 ACATCCAAATTTG-CAAATAACTCCGTTTCAAGGAAGAAAACACACCAAATGAGGATTTTGGAGT

             *           
       8506 CGCATGCAAATTT
         65 CACATGCAAATTT

       8519 GCTAACAGAA


Statistics
Matches: 71,  Mismatches: 6, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  77   13  0.18
  78   58  0.82

ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26


Consensus pattern (77 bp):   
ACATCCAAATTTGCAAATAACTCCGTTTCAAGGAAGAAAACACACCAAATGAGGATTTTGGAGTC
ACATGCAAATTT

Found at i:8519 original size:143 final size:142

Alignment explanation


    Indices: 8262--8520  Score: 401
    Period size: 143  Copynumber: 1.8  Consensus size: 142

       8252 CAATTGAGAA

                   *                                           *       **    
       8262 CACACTAGATGAGGATTTTGGAGTCACATGCAAATTTACATCCAAATTTGCTAATAACTTTGTTT
          1 CACACTAAATGAGGATTTTGGAGTCACATGCAAATTTACATCCAAATTTGCAAATAACTCCGTTT

                       **    **                                              
       8327 GAAGAAAGAAAGTACACTGGATGAGGATTTTGGAGTCACATCCAAATTTGCAAATAACTCCGTTT
         66 GAAGAAAGAAAACACACCAGATGAGGATTTTGGAGTCACATCCAAATTTGCAAATAACTCCGTTT

                        
       8392 CAAGGAAGAAAG
        131 CAAGGAAGAAAG

                      *                                                      
       8404 CACACTAAATTAGGATTTTGGAGTCACATGCAAATTTACATCCAAATTTGCCAAATAACTCCGTT
          1 CACACTAAATGAGGATTTTGGAGTCACATGCAAATTTACATCCAAATTTG-CAAATAACTCCGTT

                 *                                *   *         
       8469 TGAAGGAAGAAAACACACCAGATGAGGATTTTGGAGTCGCATGCAAATTTGC
         65 TGAAGAAAGAAAACACACCAGATGAGGATTTTGGAGTCACATCCAAATTTGC

       8521 TAACAGAAAG


Statistics
Matches: 104,  Mismatches: 12, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
 142   48  0.46
 143   56  0.54

ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27


Consensus pattern (142 bp):   
CACACTAAATGAGGATTTTGGAGTCACATGCAAATTTACATCCAAATTTGCAAATAACTCCGTTT
GAAGAAAGAAAACACACCAGATGAGGATTTTGGAGTCACATCCAAATTTGCAAATAACTCCGTTT
CAAGGAAGAAAG
Done.