Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000063.1 Kokia drynarioides strain JFW-HI SEQ_110606, 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: 40979
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:2021 original size:2 final size:2

Alignment explanation


    Indices: 2014--2044  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2004 AAATTTGTAA

                                                          
       2014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2045 AAATCTGTGT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:6258 original size:180 final size:179

Alignment explanation


    Indices: 5957--6315  Score: 648
    Period size: 180  Copynumber: 2.0  Consensus size: 179

       5947 ATAGAGACAA

                                                                        *    
       5957 TTTCAGGTGGGTGAAAACAGTTCGTCAACTTAAAGAAAGAACTAACTCAAGACAAATGCAGCTTA
          1 TTTCAGGTGGGTGAAAACAGTTCGTCAACTTAAAGAAAGAACTAACTCAAGACAAATGCAACTTA

                                             *                               
       6022 CATGCTCCCATTGAGAATAACTATTAACTACATTACCATGACAGACTAGACTGTAAATACAAAGA
         66 CATGCTCCCATTGAGAATAACTATTAACTACATCACCATGACAGACTAGACTGTAAATACAAAGA

                                                      *      
       6087 ATAAAAAAAGGATCTTTATACAAGATTTTTCTTACTTTCACGGTCCCCT
        131 ATAAAAAAAGGATCTTTATACAAGATTTTTCTTACTTTCACGATCCCCT

                                                                             
       6136 TTTCAGGTGGGTGAAAACAGTTCGTCAACTTAAAAGAAAGAA-TCAACTCAAGACAAATGCAACT
          1 TTTCAGGTGGGTGAAAACAGTTCGTCAACTT-AAAGAAAGAACT-AACTCAAGACAAATGCAACT

                  *                         *                                
       6200 TACATGTTCCCATTGAGAATAACTATTAACTATATCACCATGACAGACTAGACTGTAAATACAAA
         64 TACATGCTCCCATTGAGAATAACTATTAACTACATCACCATGACAGACTAGACTGTAAATACAAA

                                                               
       6265 GAATAAAAAAAGGATCTTTATACAAGATTTTTCTTACTTTCACGATCCCCT
        129 GAATAAAAAAAGGATCTTTATACAAGATTTTTCTTACTTTCACGATCCCCT

       6316 AGTAATCATT


Statistics
Matches: 173,  Mismatches: 5, Indels: 3
        0.96            0.03        0.02

Matches are distributed among these distances:
 179   32  0.18
 180  141  0.82

ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28


Consensus pattern (179 bp):   
TTTCAGGTGGGTGAAAACAGTTCGTCAACTTAAAGAAAGAACTAACTCAAGACAAATGCAACTTA
CATGCTCCCATTGAGAATAACTATTAACTACATCACCATGACAGACTAGACTGTAAATACAAAGA
ATAAAAAAAGGATCTTTATACAAGATTTTTCTTACTTTCACGATCCCCT

Found at i:14443 original size:12 final size:12

Alignment explanation


    Indices: 14417--14450  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

      14407 TTGTTTATTT

                      *  
      14417 AACATTGTTCGTG
          1 AACA-TGTTCATG

                        
      14430 AACATGTTCATG
          1 AACATGTTCATG

                     
      14442 AACATGTTC
          1 AACATGTTC

      14451 GTTTAATGGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   16  0.80
  13    4  0.20

ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35


Consensus pattern (12 bp):   
AACATGTTCATG

Found at i:28875 original size:60 final size:59

Alignment explanation


    Indices: 28807--28941  Score: 155
    Period size: 60  Copynumber: 2.3  Consensus size: 59

      28797 TTTGATCCTA

                            *     *   *     **                *         
      28807 AATT-TAAAATTTTAATAAATTTAACTTTCAATGTTTACAAAATTTATCATTTTAGTTCT
          1 AATTCTAAAATTTTAAGAAA-TCAACCTTCAACATTTACAAAATTTATCAATTTAGTTCT

                       *  *                       *       *             
      28866 AATTCTAAAAAATTCAAGAAATCAACCTTCAACATTTATAAAATTTGTCAATTTAGTTCT
          1 AATTCT-AAAATTTTAAGAAATCAACCTTCAACATTTACAAAATTTATCAATTTAGTTCT

                            
      28926 AATTCTAAAATTTTAA
          1 AATTCTAAAATTTTAA

      28942 AAAAAAATGT


Statistics
Matches: 62,  Mismatches: 12, Indels: 4
        0.79            0.15        0.05

Matches are distributed among these distances:
  59   12  0.19
  60   39  0.63
  61   11  0.18

ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43


Consensus pattern (59 bp):   
AATTCTAAAATTTTAAGAAATCAACCTTCAACATTTACAAAATTTATCAATTTAGTTCT

Found at i:29329 original size:20 final size:20

Alignment explanation


    Indices: 29277--29329  Score: 60
    Period size: 17  Copynumber: 2.8  Consensus size: 20

      29267 AAATTCAATG

                                
      29277 AATAATTAAAA-AT--AAAT
          1 AATAATTAAAAGATAAAAAT

                      *         
      29294 AATAATTAAATGATAAAAAT
          1 AATAATTAAAAGATAAAAAT

                             
      29314 AA-AATTAAAAGTATAA
          1 AATAATTAAAAG-ATAA

      29330 TTGAGTAACT


Statistics
Matches: 30,  Mismatches: 2, Indels: 5
        0.81            0.05        0.14

Matches are distributed among these distances:
  17   10  0.33
  18    2  0.07
  19    8  0.27
  20   10  0.33

ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28


Consensus pattern (20 bp):   
AATAATTAAAAGATAAAAAT

Found at i:40133 original size:5 final size:5

Alignment explanation


    Indices: 40123--40147  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

      40113 ATTTCGAAAG

                                         
      40123 TAAAA TAAAA TAAAA TAAAA TAAAA
          1 TAAAA TAAAA TAAAA TAAAA TAAAA

      40148 AAAGAAAAAG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (5 bp):   
TAAAA

Done.