Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009411.1 Kokia drynarioides strain JFW-HI SEQ_124118, 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, 653

Length: 1089
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39


Found at i:375 original size:216 final size:215

Alignment explanation


    Indices: 1--470  Score: 640
    Period size: 216  Copynumber: 2.2  Consensus size: 215

                                      * *    *                **             
          1 TCTCTCTTGGTTCTTGGACGAACATCCGTACTTTTCAAACTTTTACAATTTTTTTTATAACTTCG
          1 TCTCTCTTGGTTCTTGGACGAACATCTGAACTTATCAAACTTTTACAATTACTTTTATAACTTCG

                                *                       ***                * 
         66 GTTCCTGAAAGTATTCAGGAGGATCCAATCCTTTGAGCAATTTTTTGAACATTCCATGCTCGGGA
         66 GTTCCTGAAAGTATTCAGGACGATCCAATCCTTTGAGCAATTTTCCAAACATTCCATGCTCGGAA

                                                              *              
        131 AATCGCATAATTTGGTCTTAAAAGTTTGTC-TTTCGGTAAACAA-ATTTTTGTCGCTGAATTAAA
        131 AATCGCATAATTTGGTCTTAAAAGTTTGTCATTT-GG-AAA-AATATTTTAGTCGCTGAATTAAA

                              *    
        194 AACTTATTTACATGAAAATTGGT
        193 AACTTATTTACATGAAAACTGGT

                                             *            *                  
        217 TCTCTCTTGGTTCTTGGACGAACATCTGAACTTGTCAAACTTTTACGATTACTTTTATAACTTCG
          1 TCTCTCTTGGTTCTTGGACGAACATCTGAACTTATCAAACTTTTACAATTACTTTTATAACTTCG

                             *         *          *                *         
        282 GTTCCTGAAAGTATTCATGACGATCCATTCCTTTGAGCTATTTTCCAAACATTCCTTGCTCGGAA
         66 GTTCCTGAAAGTATTCAGGACGATCCAATCCTTTGAGCAATTTTCCAAACATTCCATGCTCGGAA

                    *                          *                **           
        347 AATCGCATGATTTGGTC-TAAATAGTTTGTCATTTTGAAAAATATTTTAGTCTTTGAATTAAAAA
        131 AATCGCATAATTTGGTCTTAAA-AGTTTGTCATTTGGAAAAATATTTTAGTCGCTGAATTAAAAA

                         *     * 
        411 CTTATTTACATGACAACTGTT
        195 CTTATTTACATGAAAACTGGT

                            * *    *               
        432 TCTCTCTTGGTTCTTGTAAGAACTTCTGAACTTATCAAA
          1 TCTCTCTTGGTTCTTGGACGAACATCTGAACTTATCAAA

        471 AACTTATTTA


Statistics
Matches: 224,  Mismatches: 27, Indels: 7
        0.87            0.10        0.03

Matches are distributed among these distances:
 214    2  0.01
 215   79  0.35
 216  140  0.62
 217    3  0.01

ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40


Consensus pattern (215 bp):   
TCTCTCTTGGTTCTTGGACGAACATCTGAACTTATCAAACTTTTACAATTACTTTTATAACTTCG
GTTCCTGAAAGTATTCAGGACGATCCAATCCTTTGAGCAATTTTCCAAACATTCCATGCTCGGAA
AATCGCATAATTTGGTCTTAAAAGTTTGTCATTTGGAAAAATATTTTAGTCGCTGAATTAAAAAC
TTATTTACATGAAAACTGGT

Found at i:760 original size:62 final size:62

Alignment explanation


    Indices: 676--845  Score: 268
    Period size: 62  Copynumber: 2.7  Consensus size: 62

        666 GTTAATTAAT

                  *   *  *                       *                        
        676 AACTTAGTTAGGTAAGAATTGTTTCTCTCTTGGTTCTGGGACGAACTTCCAAACTTATCAAA
          1 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTATCAAA

                                          *                         *  *  
        738 AACTTATTTACGTGAGAATTGTTTCTCTCTGGGTTCTTGGACGAACTTCCAAACTTGTCGAA
          1 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTATCAAA

                                        *                 
        800 AACTTATTTACGTGAGAATTGTTTCTCTGTTGGTTCTTGGACGAAC
          1 AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAAC

        846 ATCCGTACTT


Statistics
Matches: 99,  Mismatches: 9, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  62   99  1.00

ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38


Consensus pattern (62 bp):   
AACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCAAACTTATCAAA
Done.