Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010478.1 Kokia drynarioides strain JFW-HI SEQ_125379, 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: 4800
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:438 original size:15 final size:15

Alignment explanation


    Indices: 420--490  Score: 115
    Period size: 15  Copynumber: 4.7  Consensus size: 15

        410 TTTTGGGTAG

                           
        420 TTTGTAATTGGGCCA
          1 TTTGTAATTGGGCCA

                  *        
        435 TTTGTATTTGGGCCA
          1 TTTGTAATTGGGCCA

             *             
        450 TCTGTAATTGGGCCA
          1 TTTGTAATTGGGCCA

                 *         
        465 TTTGTTATTGGGCCA
          1 TTTGTAATTGGGCCA

                       
        480 TTTGTAATTGG
          1 TTTGTAATTGG

        491 ACTTTGTTTT


Statistics
Matches: 50,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   50  1.00

ACGTcount: A:0.17, C:0.13, G:0.27, T:0.44


Consensus pattern (15 bp):   
TTTGTAATTGGGCCA

Found at i:547 original size:34 final size:33

Alignment explanation


    Indices: 509--587  Score: 113
    Period size: 34  Copynumber: 2.4  Consensus size: 33

        499 TTGGACTTTT

                          *      *            
        509 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
          1 TAAATTTAATTTTAAAATAAACTTAAATTT-AAA

                     *                       
        543 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
          1 TAAATTTAATTTTAAAATAAACTTAAATTTAAA

                  *     
        576 TAAATTCAATTT
          1 TAAATTTAATTT

        588 CCAATAAGTC


Statistics
Matches: 40,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  33   13  0.32
  34   27  0.68

ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44


Consensus pattern (33 bp):   
TAAATTTAATTTTAAAATAAACTTAAATTTAAA

Found at i:560 original size:7 final size:6

Alignment explanation


    Indices: 507--576  Score: 60
    Period size: 6  Copynumber: 12.2  Consensus size: 6

        497 TTTTGGACTT

                        *                                            
        507 TTTAAA TTTAAT TTTATAA --TAAA TTTAAA TTTCAAA --TAAA TTTAAA
          1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA

                    *     *              
        553 TTTAAA -ATAAA CTTAAA TTTAAA T
          1 TTTAAA TTTAAA TTTAAA TTTAAA T

        577 AAATTCAATT


Statistics
Matches: 52,  Mismatches: 5, Indels: 14
        0.73            0.07        0.20

Matches are distributed among these distances:
   4    5  0.10
   5    7  0.13
   6   36  0.69
   7    4  0.08

ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46


Consensus pattern (6 bp):   
TTTAAA

Found at i:593 original size:16 final size:17

Alignment explanation


    Indices: 509--594  Score: 97
    Period size: 17  Copynumber: 5.2  Consensus size: 17

        499 TTGGACTTTT

                         *    
        509 TAAATTT-AATTTTATAA
          1 TAAATTTAAATTTCA-AA

                             
        526 TAAATTTAAATTTCAAA
          1 TAAATTTAAATTTCAAA

                         *   
        543 TAAATTTAAATTTAAAA
          1 TAAATTTAAATTTCAAA

                *            
        560 TAAACTTAAATTT-AAA
          1 TAAATTTAAATTTCAAA

                   *      *  
        576 TAAA-TTCAATTTCCAA
          1 TAAATTTAAATTTCAAA

               
        592 TAA
          1 TAA

        595 GTCCAGACAA


Statistics
Matches: 62,  Mismatches: 5, Indels: 5
        0.86            0.07        0.07

Matches are distributed among these distances:
  15    7  0.11
  16   12  0.19
  17   37  0.60
  18    6  0.10

ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42


Consensus pattern (17 bp):   
TAAATTTAAATTTCAAA

Found at i:4404 original size:18 final size:18

Alignment explanation


    Indices: 4383--4451  Score: 61
    Period size: 18  Copynumber: 3.8  Consensus size: 18

       4373 TTTATATATT

                              
       4383 TTTTATAATTTTTATAAA
          1 TTTTATAATTTTTATAAA

                 *  ** *      
       4401 TTTTAAAAAATATATAAA
          1 TTTTATAATTTTTATAAA

                               
       4419 TTTTGA-AATTTTTATAAA
          1 TTTT-ATAATTTTTATAAA

                   *        
       4437 TATTT-TGATTTTTAT
          1 T-TTTATAATTTTTAT

       4452 TTTTCTAATT


Statistics
Matches: 40,  Mismatches: 8, Indels: 6
        0.74            0.15        0.11

Matches are distributed among these distances:
  18   36  0.90
  19    4  0.10

ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57


Consensus pattern (18 bp):   
TTTTATAATTTTTATAAA
Done.