Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003517.1 Kokia drynarioides strain JFW-HI SEQ_116357, 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, 709

Length: 1183
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35


Found at i:85 original size:16 final size:17

Alignment explanation


    Indices: 50--92  Score: 52
    Period size: 16  Copynumber: 2.6  Consensus size: 17

         40 AACTATGAAA

                          *  
         50 ACAAATAAAATGCAGGG
          1 ACAAATAAAATGCAAGG

                           * 
         67 ACAAA-AAAATGCAATG
          1 ACAAATAAAATGCAAGG

                *     
         83 ACAATTAAAA
          1 ACAAATAAAA

         93 GAAATGCATG


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  16   13  0.59
  17    9  0.41

ACGTcount: A:0.60, C:0.12, G:0.14, T:0.14


Consensus pattern (17 bp):   
ACAAATAAAATGCAAGG

Found at i:501 original size:9 final size:9

Alignment explanation


    Indices: 487--543  Score: 50
    Period size: 9  Copynumber: 6.7  Consensus size: 9

        477 AGGCAACATA

                     
        487 TTCTTCTCT
          1 TTCTTCTCT

                     
        496 TTCTTC-CT
          1 TTCTTCTCT

                    * 
        504 TCTCTTCTTT
          1 T-TCTTCTCT

                     
        514 TTC-T-TC-
          1 TTCTTCTCT

                 *   
        520 TTCTTTTCT
          1 TTCTTCTCT

                    *
        529 TTCTTCTCC
          1 TTCTTCTCT

                  
        538 TTCTTC
          1 TTCTTC

        544 CTCAATACCC


Statistics
Matches: 39,  Mismatches: 4, Indels: 10
        0.74            0.08        0.19

Matches are distributed among these distances:
   6    3  0.08
   7    2  0.05
   8    6  0.15
   9   26  0.67
  10    2  0.05

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (9 bp):   
TTCTTCTCT

Found at i:535 original size:18 final size:17

Alignment explanation


    Indices: 487--542  Score: 62
    Period size: 17  Copynumber: 3.3  Consensus size: 17

        477 AGGCAACATA

                 *           
        487 TTCTTCTCTTTCTTC-C
          1 TTCTTTTCTTTCTTCTC

                *             
        503 TTCTCTTCTTT-TTCTTC
          1 TTCTTTTCTTTCTTC-TC

                              
        520 TTCTTTTCTTTCTTCTCC
          1 TTCTTTTCTTTCTTCT-C

                 
        538 TTCTT
          1 TTCTT

        543 CCTCAATACC


Statistics
Matches: 33,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  15    3  0.09
  16    9  0.27
  17   12  0.36
  18    9  0.27

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (17 bp):   
TTCTTTTCTTTCTTCTC
Done.