Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008962.1 Kokia drynarioides strain JFW-HI SEQ_123658, 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: 6481
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33


Found at i:265 original size:33 final size:31

Alignment explanation


    Indices: 205--265  Score: 77
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        195 AATAAAGTTT

                *       *                  
        205 TTTTTTTTTATCTTAAATTTAATTATTTAAA
          1 TTTTATTTTATCCTAAATTTAATTATTTAAA

                                  *       
        236 TTTTATTTTATCCTAATATTTTTATTATTT
          1 TTTTATTTTATCCTAA-A-TTTAATTATTT

        266 TGCGTAAATT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  31   14  0.56
  32    1  0.04
  33   10  0.40

ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67


Consensus pattern (31 bp):   
TTTTATTTTATCCTAAATTTAATTATTTAAA

Found at i:5215 original size:41 final size:41

Alignment explanation


    Indices: 5156--5276  Score: 197
    Period size: 41  Copynumber: 3.0  Consensus size: 41

       5146 CGCGGCGCTT

                *                                    
       5156 GTCAGGGCATTAGCGGCGCTTTCCCATAAGCGCCGCTAAAG
          1 GTCAAGGCATTAGCGGCGCTTTCCCATAAGCGCCGCTAAAG

                                           *         
       5197 GTCAAGGCATTAGCGGCGCTTTCCCATAAGCCCCGCTAAAG
          1 GTCAAGGCATTAGCGGCGCTTTCCCATAAGCGCCGCTAAAG

                   *              * *              
       5238 GTCAAGGTATTAGCGGCGCTTTTCGATAAGCGCCGCTAA
          1 GTCAAGGCATTAGCGGCGCTTTCCCATAAGCGCCGCTAA

       5277 TTTATTTAAA


Statistics
Matches: 74,  Mismatches: 6, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  41   74  1.00

ACGTcount: A:0.23, C:0.28, G:0.27, T:0.21


Consensus pattern (41 bp):   
GTCAAGGCATTAGCGGCGCTTTCCCATAAGCGCCGCTAAAG

Found at i:6178 original size:170 final size:169

Alignment explanation


    Indices: 5896--6283  Score: 632
    Period size: 170  Copynumber: 2.3  Consensus size: 169

       5886 TGTGTACAAT

                                                  *                          
       5896 TTCTTATAGTACTGTTCGGGAGGTCGATAAGCTAATTCTCGTGGATGTCTATACAGTAACAATGA
          1 TTCTTATAGTACTGTTCGGG-GGTCGATAAGCTAATTCCCGTGGATGTCTATACAGTAACAATGA

                    *                                                        
       5961 AAATGGCGTCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATGTTATTGCTA
         65 AAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATGTTATTGCTA

                   *          *                     
       6026 TGGGCGCGTGTACAATTATAGGAGGGATGTTCAATACTGA
        130 TGGGCGCATGTACAATTACAGGAGGGATGTTCAATACTGA

                                     *                                       
       6066 TTCTTATAGTACTGTTCGAGGGGTCAATAAGCTAATTCCCGTGGATGTCTATACAGTAACAATGA
          1 TTCTTATAGTACTGTTCG-GGGGTCGATAAGCTAATTCCCGTGGATGTCTATACAGTAACAATGA

                                     *                                    * *
       6131 AAATGGCGCCCTCTTTAGTGAGATTTTATATGAACAAATGCCCGAACCTAAATATGTTATTGTTG
         65 AAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATGTTATTGCTA

                                                   *
       6196 TGGGCGCATGTACAATTACAGGAGGGATGTTCAATACTGT
        130 TGGGCGCATGTACAATTACAGGAGGGATGTTCAATACTGA

              *              *      *      *                
       6236 TTATTATAGTACTGTTTGGGGGGTGGATAAGTTAATTCCCGTGGATGT
          1 TTCTTATAGTACTG-TTCGGGGGTCGATAAGCTAATTCCCGTGGATGT

       6284 TTATTTGCCG


Statistics
Matches: 202,  Mismatches: 14, Indels: 4
        0.92            0.06        0.02

Matches are distributed among these distances:
 170  197  0.98
 171    5  0.02

ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33


Consensus pattern (169 bp):   
TTCTTATAGTACTGTTCGGGGGTCGATAAGCTAATTCCCGTGGATGTCTATACAGTAACAATGAA
AATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATGTTATTGCTAT
GGGCGCATGTACAATTACAGGAGGGATGTTCAATACTGA

Found at i:6375 original size:29 final size:27

Alignment explanation


    Indices: 6343--6441  Score: 92
    Period size: 29  Copynumber: 3.5  Consensus size: 27

       6333 TAACTAGACT

                                         
       6343 AAATATAAATAATAACTAAATAAAAATAA
          1 AAATATAAATAATAA-TAAAT-AAAATAA

                *          *            
       6372 AAATTTAAATAATATTTAAATAAAATAA
          1 AAATATAAATAATA-ATAAATAAAATAA

            *       *         *   *     
       6400 TAATAATATATAATAATAGATAGAATAA
          1 AAAT-ATAAATAATAATAAATAAAATAA

                           
       6428 TAAA-ATAAATAATA
          1 -AAATATAAATAATA

       6442 TAGAAATATA


Statistics
Matches: 57,  Mismatches: 10, Indels: 8
        0.76            0.13        0.11

Matches are distributed among these distances:
  27    9  0.16
  28   20  0.35
  29   28  0.49

ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30


Consensus pattern (27 bp):   
AAATATAAATAATAATAAATAAAATAA
Done.