Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007770.1 Kokia drynarioides strain JFW-HI SEQ_122403, 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: 14924
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32


Found at i:3877 original size:33 final size:33

Alignment explanation


    Indices: 3853--3928  Score: 134
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       3843 ACAGATGCCA

                     *                       
       3853 CAGCAGCAGGTCCCACAGCTGCAACAACAGCAG
          1 CAGCAGCAGCTCCCACAGCTGCAACAACAGCAG

                                             
       3886 CAGCAGCAGCTCCCACAGCTGCAACAACAGCAG
          1 CAGCAGCAGCTCCCACAGCTGCAACAACAGCAG

                 *    
       3919 CAGCAACAGC
          1 CAGCAGCAGC

       3929 CACAGCAGCA


Statistics
Matches: 41,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  33   41  1.00

ACGTcount: A:0.34, C:0.38, G:0.22, T:0.05


Consensus pattern (33 bp):   
CAGCAGCAGCTCCCACAGCTGCAACAACAGCAG

Found at i:3934 original size:12 final size:12

Alignment explanation


    Indices: 3868--3943  Score: 53
    Period size: 12  Copynumber: 6.1  Consensus size: 12

       3858 GCAGGTCCCA

                *      *
       3868 CAGCTGCAACAA
          1 CAGCAGCAACAG

                    *   
       3880 CAGCAGCAGCAG
          1 CAGCAGCAACAG

                ** *    
       3892 CAGCTCCCACAG
          1 CAGCAGCAACAG

             *   *      
       3904 CTGCAACAACAG
          1 CAGCAGCAACAG

                        
       3916 CAGCAGCAACAG
          1 CAGCAGCAACAG

                           
       3928 CCACAGCAGCAACAG
          1 ---CAGCAGCAACAG

             
       3943 C
          1 C

       3944 CGCTCCCACA


Statistics
Matches: 48,  Mismatches: 13, Indels: 6
        0.72            0.19        0.09

Matches are distributed among these distances:
  12   36  0.75
  15   12  0.25

ACGTcount: A:0.37, C:0.38, G:0.21, T:0.04


Consensus pattern (12 bp):   
CAGCAGCAACAG

Found at i:3934 original size:15 final size:15

Alignment explanation


    Indices: 3898--3944  Score: 60
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       3888 GCAGCAGCTC

                   *       
       3898 CCACAGCTGCAACA-
          1 CCACAGCAGCAACAG

            *               
       3912 ACAGCAGCAGCAACAG
          1 CCA-CAGCAGCAACAG

                           
       3928 CCACAGCAGCAACAG
          1 CCACAGCAGCAACAG

              
       3943 CC
          1 CC

       3945 GCTCCCACAT


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  14    2  0.07
  15   24  0.86
  16    2  0.07

ACGTcount: A:0.38, C:0.40, G:0.19, T:0.02


Consensus pattern (15 bp):   
CCACAGCAGCAACAG

Found at i:4019 original size:39 final size:39

Alignment explanation


    Indices: 3961--4035  Score: 107
    Period size: 39  Copynumber: 1.9  Consensus size: 39

       3951 ACATTTGCAA

                                   *     *         
       3961 CAGCAACAACTCCCTCAGCTGCAGCAACAGCAGCAGCAG
          1 CAGCAACAACTCCCTCAGCTGCAACAACAACAGCAGCAG

                 *                               
       4000 CAGCAGCAACTCTCC-CAGCTGCAACAACAACAGCAG
          1 CAGCAACAACTC-CCTCAGCTGCAACAACAACAGCAG

       4036 TTGCCCCAGC


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  39   30  0.94
  40    2  0.06

ACGTcount: A:0.35, C:0.39, G:0.19, T:0.08


Consensus pattern (39 bp):   
CAGCAACAACTCCCTCAGCTGCAACAACAACAGCAGCAG

Found at i:5741 original size:52 final size:52

Alignment explanation


    Indices: 5684--5785  Score: 179
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       5674 AAGGGGGTTT

                                                                 
       5684 AGTGATGAAAATATTAAACAAAAAAA-AAACTAAAATAAAATGAAATAAATAA
          1 AGTGATGAAAATATTAAACAAAAAAACAAACTAAAATAAAAT-AAATAAATAA

                                                              
       5736 AGTGATGAAAATATTAAACAAAAAAACTAAACTAAAATAAAATAAATAAA
          1 AGTGATGAAAATATTAAACAAAAAAAC-AAACTAAAATAAAATAAATAAA

       5786 GTGAAAATGA


Statistics
Matches: 48,  Mismatches: 0, Indels: 3
        0.94            0.00        0.06

Matches are distributed among these distances:
  52   26  0.54
  53    7  0.15
  54   15  0.31

ACGTcount: A:0.69, C:0.05, G:0.07, T:0.20


Consensus pattern (52 bp):   
AGTGATGAAAATATTAAACAAAAAAACAAACTAAAATAAAATAAATAAATAA

Found at i:5779 original size:49 final size:50

Alignment explanation


    Indices: 5684--5789  Score: 169
    Period size: 49  Copynumber: 2.1  Consensus size: 50

       5674 AAGGGGGTTT

                                                     *          
       5684 AGTGATGAAAATATTAAACAAAAAAAAAACTAAAATAAAATGAAATAAATAA
          1 AGTGATGAAAATATTAAAC--AAAAAAAACTAAAATAAAATAAAATAAATAA

                                            *                 
       5736 AGTGATGAAAATATTAAAC-AAAAAAACTAAACTAAAATAAAATAAATAA
          1 AGTGATGAAAATATTAAACAAAAAAAACTAAAATAAAATAAAATAAATAA

                 
       5785 AGTGA
          1 AGTGA

       5790 AAATGAAGTT


Statistics
Matches: 52,  Mismatches: 2, Indels: 3
        0.91            0.04        0.05

Matches are distributed among these distances:
  49   33  0.63
  52   19  0.37

ACGTcount: A:0.67, C:0.05, G:0.08, T:0.20


Consensus pattern (50 bp):   
AGTGATGAAAATATTAAACAAAAAAAACTAAAATAAAATAAAATAAATAA

Done.