Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003637.1 Kokia drynarioides strain JFW-HI SEQ_116535, 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: 15488
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33


Found at i:6661 original size:24 final size:24

Alignment explanation


    Indices: 6629--6697  Score: 102
    Period size: 24  Copynumber: 2.9  Consensus size: 24

       6619 TAGACTAATA

                       *            
       6629 AGAGTTTAACTCAAACAATTAAAC
          1 AGAGTTTAACTGAAACAATTAAAC

                                    
       6653 AGAGTTTAACTGAAACAATTAAAC
          1 AGAGTTTAACTGAAACAATTAAAC

             *    *        *     
       6677 ATAGTTAAACTGAAAGAATTA
          1 AGAGTTTAACTGAAACAATTA

       6698 TTTCTCAAAT


Statistics
Matches: 41,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   41  1.00

ACGTcount: A:0.51, C:0.12, G:0.12, T:0.26


Consensus pattern (24 bp):   
AGAGTTTAACTGAAACAATTAAAC

Found at i:9906 original size:113 final size:109

Alignment explanation


    Indices: 9776--9998  Score: 401
    Period size: 113  Copynumber: 2.0  Consensus size: 109

       9766 AAGTGTCGCT

                                                                             
       9776 ACTTTAACAAAAAAATACAATCTCCCATAATACAAAAGGTCAAAACTTAAATAAAGGTCATGTAT
          1 ACTTTAACAAAAAAATACAATCTCCCATAATACAAAAGGTCAAAACTTAAATAAAGGTCATGTAT

                                                            
       9841 TAGTGTCACGGGCTAGCTAGTGTTCAAACCCCGTGACCATTACACCAA
         66 TAGTGTCAC-GG---GCTAGTGTTCAAACCCCGTGACCATTACACCAA

                                              *                              
       9889 ACTTTAACAAAAAAATACAATCTCCCATAATACATAAGGTCAAAACTTAAATAAAGGTCATGTAT
          1 ACTTTAACAAAAAAATACAATCTCCCATAATACAAAAGGTCAAAACTTAAATAAAGGTCATGTAT

                                                        
       9954 TAGTGTCACGGGCTAGTGTTCAAACCCCGTGACCATTACACCAA
         66 TAGTGTCACGGGCTAGTGTTCAAACCCCGTGACCATTACACCAA

             
       9998 A
          1 A

       9999 TGTGTCCTAA


Statistics
Matches: 109,  Mismatches: 1, Indels: 4
        0.96            0.01        0.04

Matches are distributed among these distances:
 109   34  0.31
 112    2  0.02
 113   73  0.67

ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24


Consensus pattern (109 bp):   
ACTTTAACAAAAAAATACAATCTCCCATAATACAAAAGGTCAAAACTTAAATAAAGGTCATGTAT
TAGTGTCACGGGCTAGTGTTCAAACCCCGTGACCATTACACCAA

Found at i:12948 original size:17 final size:18

Alignment explanation


    Indices: 12920--12953  Score: 61
    Period size: 17  Copynumber: 1.9  Consensus size: 18

      12910 TTTTTTTTCT

                              
      12920 TCTTCTTTCTTTCCATCG
          1 TCTTCTTTCTTTCCATCG

                             
      12938 TCTTC-TTCTTTCCATC
          1 TCTTCTTTCTTTCCATC

      12954 TGTTATTGCC


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

Matches are distributed among these distances:
  17   11  0.69
  18    5  0.31

ACGTcount: A:0.06, C:0.35, G:0.03, T:0.56


Consensus pattern (18 bp):   
TCTTCTTTCTTTCCATCG

Found at i:14206 original size:2 final size:2

Alignment explanation


    Indices: 14199--14232  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      14189 ATTAAAAATC

                                                *             
      14199 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      14233 GAAAAATATG


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:14511 original size:26 final size:26

Alignment explanation


    Indices: 14480--14548  Score: 104
    Period size: 26  Copynumber: 2.7  Consensus size: 26

      14470 TATCTCGACC

                                      *
      14480 CACAGCTCGTGTGAGC-AGACCCATTT
          1 CACAGCTCGTGTGAGCAAG-CCCATTA

                                      
      14506 CACAGCTCGTGTGAGCAAGCCCATTA
          1 CACAGCTCGTGTGAGCAAGCCCATTA

            *                
      14532 GACAGCTCGTGTGAGCA
          1 CACAGCTCGTGTGAGCA

      14549 TATATGATTA


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  26   38  0.95
  27    2  0.05

ACGTcount: A:0.25, C:0.29, G:0.26, T:0.20


Consensus pattern (26 bp):   
CACAGCTCGTGTGAGCAAGCCCATTA

Found at i:15356 original size:21 final size:22

Alignment explanation


    Indices: 15323--15366  Score: 72
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      15313 TTTTGGCTAC

                                  
      15323 TACCTAGGGTTGTACTGGTAGT
          1 TACCTAGGGTTGTACTGGTAGT

                          *       
      15345 TACCTA-GGTTGTATTGGTAGT
          1 TACCTAGGGTTGTACTGGTAGT

             
      15366 T
          1 T

      15367 TGGATTTGTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  21   15  0.71
  22    6  0.29

ACGTcount: A:0.18, C:0.11, G:0.30, T:0.41


Consensus pattern (22 bp):   
TACCTAGGGTTGTACTGGTAGT
Done.