Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008556.1 Kokia drynarioides strain JFW-HI SEQ_123234, 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: 2543
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Found at i:568 original size:18 final size:18

Alignment explanation


    Indices: 547--644  Score: 89
    Period size: 17  Copynumber: 5.6  Consensus size: 18

        537 TAATAAGTTT

                       *    * 
        547 TAAATTTAAATATAAATC
          1 TAAATTTAAATTTAAAAC

                               
        565 TAAATTTAAATTTTAAAAC
          1 TAAATTTAAA-TTTAAAAC

                              
        584 -AAATTTAAATTTAAAA-
          1 TAAATTTAAATTTAAAAC

              *         *     
        600 TATATTTAAATTCAAAA-
          1 TAAATTTAAATTTAAAAC

             *                 
        617 TCAATTT-AATCTTAAAA-
          1 TAAATTTAAAT-TTAAAAC

                       
        634 TAAATCTTAAA
          1 TAAAT-TTAAA

        645 ATGGGTTTAA


Statistics
Matches: 67,  Mismatches: 8, Indels: 9
        0.80            0.10        0.11

Matches are distributed among these distances:
  16    3  0.04
  17   35  0.52
  18   21  0.31
  19    8  0.12

ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40


Consensus pattern (18 bp):   
TAAATTTAAATTTAAAAC

Found at i:573 original size:24 final size:24

Alignment explanation


    Indices: 545--598  Score: 74
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        535 TATAATAAGT

                           *         
        545 TTTAAA-TTTAAATATAAATCTAAA
          1 TTTAAATTTTAAA-ACAAATCTAAA

                               *    
        569 TTTAAATTTTAAAACAAATTTAAA
          1 TTTAAATTTTAAAACAAATCTAAA

                  
        593 TTTAAA
          1 TTTAAA

        599 ATATATTTAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  24   21  0.78
  25    6  0.22

ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43


Consensus pattern (24 bp):   
TTTAAATTTTAAAACAAATCTAAA

Found at i:600 original size:7 final size:6

Alignment explanation


    Indices: 545--611  Score: 57
    Period size: 6  Copynumber: 11.3  Consensus size: 6

        535 TATAATAAGT

                           *      *                     **          
        545 TTTAAA TTTAAA TATAAA TCTAAA TTTAAA TTTTAAA -ACAAA TTTAAA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA

                    *  *           
        593 TTTAAA -ATATA TTTAAA TT
          1 TTTAAA TTTAAA TTTAAA TT

        612 CAAAATCAAT


Statistics
Matches: 47,  Mismatches: 11, Indels: 6
        0.73            0.17        0.09

Matches are distributed among these distances:
   5    6  0.13
   6   35  0.74
   7    6  0.13

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45


Consensus pattern (6 bp):   
TTTAAA

Found at i:1766 original size:17 final size:17

Alignment explanation


    Indices: 1739--1780  Score: 75
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       1729 GGACAAAGTA

                              
       1739 GTTACAAGAATATGAAAG
          1 GTTA-AAGAATATGAAAG

                             
       1757 GTTAAAGAATATGAAAG
          1 GTTAAAGAATATGAAAG

                   
       1774 GTTAAAG
          1 GTTAAAG

       1781 GTCAAGGGAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  17   20  0.83
  18    4  0.17

ACGTcount: A:0.50, C:0.02, G:0.24, T:0.24


Consensus pattern (17 bp):   
GTTAAAGAATATGAAAG
Done.