Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004195.1 Kokia drynarioides strain JFW-HI SEQ_117430, 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: 27761
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3196 original size:13 final size:13

Alignment explanation


    Indices: 3177--3205  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       3167 TTTTCACTTC

                         
       3177 TACTTTTTATT-T
          1 TACTTTTTATTAT

                         
       3189 TACTTTTTATTAT
          1 TACTTTTTATTAT

                
       3202 TACT
          1 TACT

       3206 GTAATAATTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   11  0.69
  13    5  0.31

ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69


Consensus pattern (13 bp):   
TACTTTTTATTAT

Found at i:4108 original size:31 final size:32

Alignment explanation


    Indices: 4073--4141  Score: 77
    Period size: 31  Copynumber: 2.2  Consensus size: 32

       4063 TATAAAATAT

                    *    *                  
       4073 TCATTGAATTATTTGAAAATTTTCA-TTTAAG
          1 TCATTGAACTATTCGAAAATTTTCATTTTAAG

                 *            *    *        
       4104 TCATTAAACTATTCGAAAGTTTTTATTTTAAG
          1 TCATTGAACTATTCGAAAATTTTCATTTTAAG

            *     
       4136 CCATTG
          1 TCATTG

       4142 GGTGGTTAAA


Statistics
Matches: 30,  Mismatches: 7, Indels: 1
        0.79            0.18        0.03

Matches are distributed among these distances:
  31   20  0.67
  32   10  0.33

ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46


Consensus pattern (32 bp):   
TCATTGAACTATTCGAAAATTTTCATTTTAAG

Found at i:6614 original size:17 final size:17

Alignment explanation


    Indices: 6587--6620  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       6577 AAGGGCGTTA

                             
       6587 ACGTTCAGGTCA-TTTT
          1 ACGTTCAGGTCAGTTTT

                              
       6603 ACGTTGCAGGTCAGTTTT
          1 ACGTT-CAGGTCAGTTTT

       6621 TCCCCATGAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    5  0.31
  17    7  0.44
  18    4  0.25

ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41


Consensus pattern (17 bp):   
ACGTTCAGGTCAGTTTT

Found at i:19434 original size:12 final size:12

Alignment explanation


    Indices: 19417--19444  Score: 56
    Period size: 12  Copynumber: 2.3  Consensus size: 12

      19407 TTTTTTTTAA

                        
      19417 AAAAAAAAAAAG
          1 AAAAAAAAAAAG

                        
      19429 AAAAAAAAAAAG
          1 AAAAAAAAAAAG

                
      19441 AAAA
          1 AAAA

      19445 GCTAAAACCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00


Consensus pattern (12 bp):   
AAAAAAAAAAAG

Found at i:25801 original size:15 final size:16

Alignment explanation


    Indices: 25765--25799  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      25755 TGTGGGAAAG

                 *          
      25765 AAAATTGAAGGGTGAA
          1 AAAATAGAAGGGTGAA

                       *    
      25781 AAAATAGAAGGTTGAA
          1 AAAATAGAAGGGTGAA

               
      25797 AAA
          1 AAA

      25800 TATATATTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17


Consensus pattern (16 bp):   
AAAATAGAAGGGTGAA
Done.