Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007778.1 Kokia drynarioides strain JFW-HI SEQ_122412, 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: 8696
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34


Found at i:929 original size:84 final size:84

Alignment explanation


    Indices: 727--922  Score: 254
    Period size: 84  Copynumber: 2.3  Consensus size: 84

        717 AGTTTCCATA

                                *                                            
        727 TATTTTATTCTCTTTCCTTTACCATATTTGA-TTCTCTATTTTCCATAAAATATTAAATTCCCTT
          1 TATTTTATTCTCTTTCCTTTCCCATATTTGACTT-TCTATTTTCCATAAAATATTAAATTCCCTT

                           *  * 
        791 TCATATATCTATTTTTCACG
         65 TCATATATCTATTTTACAAG

               *                 **            *                  *    *     
        811 TATGTTATTCTCTTTCCTTTCTTATATTTGACTTTTTATTTTCCATAAAATATTTAATTTCCTTT
          1 TATTTTATTCTCTTTCCTTTCCCATATTTGACTTTCTATTTTCCATAAAATATTAAATTCCCTTT

                                 
        876 CATATCA-CTATTTTACATAG
         66 CATAT-ATCTATTTTACA-AG

                            *           
        896 T-TTTTATTCTCTTTCTTTTCCCATATT
          1 TATTTTATTCTCTTTCCTTTCCCATATT

        923 CAACTTTCCC


Statistics
Matches: 96,  Mismatches: 13, Indels: 6
        0.83            0.11        0.05

Matches are distributed among these distances:
  84   91  0.95
  85    5  0.05

ACGTcount: A:0.23, C:0.19, G:0.03, T:0.56


Consensus pattern (84 bp):   
TATTTTATTCTCTTTCCTTTCCCATATTTGACTTTCTATTTTCCATAAAATATTAAATTCCCTTT
CATATATCTATTTTACAAG

Found at i:2507 original size:91 final size:89

Alignment explanation


    Indices: 2333--2508  Score: 192
    Period size: 91  Copynumber: 2.0  Consensus size: 89

       2323 ACACTCTAGT

                               * *                        *    *             
       2333 TTGTGGATAAACCACAGTGTTGTAAGGTAATACGCTGCCAATAGTTGTGAATACACAACGAGTTT
          1 TTGTGGATAAACCACAGTGCTCTAAGGTAATACGCTGCCAATAGTTATGAACACACAACGAGTTT

             * *    *    *          
       2398 GTAGATAATAGTCGCCAGTATAAG
         66 GCAAATAACAGTCACCAGTATAAG

                           *        *                 *                 * *  
       2422 TTGTGGATAAACCAAGAGTGCTCTTAGGTTAATACGCTGCCAGTAGTTATGAACACACAATGGGT
          1 TTGTGGATAAACC-ACAGTGCTCTAAGG-TAATACGCTGCCAATAGTTATGAACACACAACGAGT

                    *              
       2487 TTGCAAATTACAG-CTACCAGTA
         64 TTGCAAATAACAGTC-ACCAGTA

       2509 ATTTATGGAT


Statistics
Matches: 70,  Mismatches: 14, Indels: 4
        0.80            0.16        0.05

Matches are distributed among these distances:
  89   13  0.19
  90   11  0.16
  91   46  0.66

ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28


Consensus pattern (89 bp):   
TTGTGGATAAACCACAGTGCTCTAAGGTAATACGCTGCCAATAGTTATGAACACACAACGAGTTT
GCAAATAACAGTCACCAGTATAAG

Found at i:8494 original size:67 final size:67

Alignment explanation


    Indices: 8356--8510  Score: 168
    Period size: 67  Copynumber: 2.3  Consensus size: 67

       8346 GGGAAGACCT

                  *                *       *                  *    **   *    
       8356 AACTTTCCAACATCAACATGATGTGAAAAACTTTTGCAACTTCAACATGGTGAGAGGACCCATTT
          1 AACTTTACAACATCAACATGATGGGAAAAACCTTTGCAACTTCAACATGGAGAGAAAACCAATTT

             *
       8421 CG
         66 CA

                  *     *              *        *                      *     
       8423 AACTTTGCAACACCAACATGATGGGAAGAACCTTTGTAACTTCAACATGGAGAGAAAACTAA-TT
          1 AACTTTACAACATCAACATGATGGGAAAAACCTTTGCAACTTCAACATGGAGAGAAAACCAATTT

               
       8487 CTA
         66 C-A

                       *         
       8490 AACTTTACAACTTCAACATGA
          1 AACTTTACAACATCAACATGA

       8511 CGAGAGGAGG


Statistics
Matches: 72,  Mismatches: 15, Indels: 2
        0.81            0.17        0.02

Matches are distributed among these distances:
  66    3  0.04
  67   69  0.96

ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26


Consensus pattern (67 bp):   
AACTTTACAACATCAACATGATGGGAAAAACCTTTGCAACTTCAACATGGAGAGAAAACCAATTT
CA
Done.