Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006284.1 Kokia drynarioides strain JFW-HI SEQ_120856, 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: 6127
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:1637 original size:73 final size:73

Alignment explanation


    Indices: 1558--1717  Score: 248
    Period size: 73  Copynumber: 2.2  Consensus size: 73

       1548 ATATTTTATT

                               ***        *           *                      
       1558 ATATATATCAACAAGTGTTGTGGATTGAATCTTAAATCGATCTATATCAATATCGTTTTAAACAT
          1 ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGATCGATATCAATATCGTTTTAAACAT

                    
       1623 TGTATCAA
         66 TGTATCAA

                                                   *                    *    
       1631 ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGGTCGATATCAATATCGTTTTAGACAT
          1 ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGATCGATATCAATATCGTTTTAAACAT

                    
       1696 TGTATCAA
         66 TGTATCAA

                  *       
       1704 ATATATGTCAACAA
          1 ATATATATCAACAA

       1718 ATGATAAATT


Statistics
Matches: 79,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  73   79  1.00

ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36


Consensus pattern (73 bp):   
ATATATATCAACAAGTGTTACAGATTGAATATTAAATCGATCGATATCAATATCGTTTTAAACAT
TGTATCAA

Found at i:2400 original size:18 final size:19

Alignment explanation


    Indices: 2377--2412  Score: 56
    Period size: 18  Copynumber: 1.9  Consensus size: 19

       2367 TAGGCGAAAT

                               
       2377 TAAATTATAT-ATTTTTAC
          1 TAAATTATATAATTTTTAC

                  *           
       2395 TAAATTTTATAATTTTTA
          1 TAAATTATATAATTTTTA

       2413 GAGTGTTAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    9  0.56
  19    7  0.44

ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58


Consensus pattern (19 bp):   
TAAATTATATAATTTTTAC

Found at i:6098 original size:24 final size:26

Alignment explanation


    Indices: 6071--6118  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

       6061 AGAGAAATGT

                                       
       6071 AAATG-TGATATATGA-A-ATTATGAG
          1 AAATGATGA-ATATGAGAGATTATGAG

                                    
       6095 AAATGATGAATATGAGAGATTATG
          1 AAATGATGAATATGAGAGATTATG

       6119 CCCATGTAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31


Consensus pattern (26 bp):   
AAATGATGAATATGAGAGATTATGAG

Done.