Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003375.1 Kokia drynarioides strain JFW-HI SEQ_116103, 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: 7775
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Found at i:536 original size:13 final size:12

Alignment explanation


    Indices: 508--542  Score: 52
    Period size: 13  Copynumber: 2.8  Consensus size: 12

        498 GTGTTATAAA

                        
        508 AACTAAGAAATT
          1 AACTAAGAAATT

                      *  
        520 AACTAAGTAACTT
          1 AACTAAG-AAATT

                      
        533 AACTAAGAAA
          1 AACTAAGAAA

        543 AATAAAAAGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  12    9  0.45
  13   11  0.55

ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23


Consensus pattern (12 bp):   
AACTAAGAAATT

Found at i:1892 original size:22 final size:22

Alignment explanation


    Indices: 1866--1910  Score: 65
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1856 TTTTTTAATT

                             *     
       1866 TTTAATTA-ATAATTAATAAATA
          1 TTTAATTATATAA-TAAAAAATA

                                  
       1888 TTTAATTATATAATAAAAAATA
          1 TTTAATTATATAATAAAAAATA

             
       1910 T
          1 T

       1911 ATTTTATATA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22   17  0.81
  23    4  0.19

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (22 bp):   
TTTAATTATATAATAAAAAATA

Found at i:1995 original size:28 final size:29

Alignment explanation


    Indices: 1945--2006  Score: 74
    Period size: 28  Copynumber: 2.2  Consensus size: 29

       1935 AAATATTTTT

                      *   *  *            
       1945 AATTAATAACTTATTTATTTATATATAT-A
          1 AATTAATAACATATGTAATTATATA-ATGA

                                         
       1974 AATTAATAA-ATATGTAATTATATAATGA
          1 AATTAATAACATATGTAATTATATAATGA

                 
       2002 AATTA
          1 AATTA

       2007 TATATTTTTG


Statistics
Matches: 29,  Mismatches: 3, Indels: 3
        0.83            0.09        0.09

Matches are distributed among these distances:
  27    2  0.07
  28   18  0.62
  29    9  0.31

ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45


Consensus pattern (29 bp):   
AATTAATAACATATGTAATTATATAATGA

Found at i:2061 original size:29 final size:31

Alignment explanation


    Indices: 2029--2097  Score: 74
    Period size: 29  Copynumber: 2.3  Consensus size: 31

       2019 TTTATCATTG

                                            
       2029 TGTTAAATATATTTTACTC-TTAT-T-TAATT
          1 TGTTAAATATATTTT-CTCTTTATATGTAATT

                **         *               
       2058 TGTTTGATATATTTTTTCTTTATATGTAATT
          1 TGTTAAATATATTTTCTCTTTATATGTAATT

                      
       2089 T-TTAAATAT
          1 TGTTAAATAT

       2098 TAAATATTTA


Statistics
Matches: 32,  Mismatches: 5, Indels: 5
        0.76            0.12        0.12

Matches are distributed among these distances:
  28    2  0.06
  29   17  0.53
  30    7  0.22
  31    6  0.19

ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61


Consensus pattern (31 bp):   
TGTTAAATATATTTTCTCTTTATATGTAATT
Done.