Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005199.1 Kokia drynarioides strain JFW-HI SEQ_119064, 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: 6712
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34


Found at i:5594 original size:21 final size:22

Alignment explanation


    Indices: 5570--5696  Score: 114
    Period size: 23  Copynumber: 5.5  Consensus size: 22

       5560 ATACAAAACA

                     *         *  
       5570 AACAGAGAGTAC-CAAAGTACT
          1 AACAGAGAGCACACAAAGTGCT

                          *    *  
       5591 AACAGAGAGCACA-TAAGTTCT
          1 AACAGAGAGCACACAAAGTGCT

                               **     
       5612 GGGCAACAGAGAGCACACACTGTGCT
          1 ----AACAGAGAGCACACAAAGTGCT

                      *            
       5638 AAACAGAGAGTACACAAAGTGCT
          1 -AACAGAGAGCACACAAAGTGCT

                                   
       5661 AATCAGAGAGCACACAAAGTGCT
          1 AA-CAGAGAGCACACAAAGTGCT

                         
       5684 AATCAGAGAGCAC
          1 AA-CAGAGAGCAC

       5697 GAGACGTGCT


Statistics
Matches: 87,  Mismatches: 12, Indels: 12
        0.78            0.11        0.11

Matches are distributed among these distances:
  21   17  0.20
  22    2  0.02
  23   51  0.59
  25   13  0.15
  26    4  0.05

ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13


Consensus pattern (22 bp):   
AACAGAGAGCACACAAAGTGCT

Found at i:5642 original size:23 final size:23

Alignment explanation


    Indices: 5616--5717  Score: 125
    Period size: 23  Copynumber: 4.4  Consensus size: 23

       5606 AGTTCTGGGC

                           **      
       5616 AACAGAGAGCACACACTGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

                     *             
       5639 AACAGAGAGTACACAAAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

             *                     
       5662 ATCAGAGAGCACACAAAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

             *             * *      
       5685 ATCAGAGAGCACGA-GACGTGCTA
          1 AACAGAGAGCAC-ACAAAGTGCTA

                      
       5708 AACAGAGAGC
          1 AACAGAGAGC

       5718 GCGCTAGTGT


Statistics
Matches: 70,  Mismatches: 8, Indels: 2
        0.88            0.10        0.03

Matches are distributed among these distances:
  23   69  0.99
  24    1  0.01

ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12


Consensus pattern (23 bp):   
AACAGAGAGCACACAAAGTGCTA

Found at i:5691 original size:69 final size:66

Alignment explanation


    Indices: 5569--5716  Score: 174
    Period size: 69  Copynumber: 2.2  Consensus size: 66

       5559 TATACAAAAC

                                               *    *                        
       5569 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTTCTGGGCAACAGAGAGCAC-ACACT
          1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACGACAC-

                 
       5633 GTGCT
         62 GTGCT

                                *                                         *  
       5638 AAACAGAGAGTACACAAAGTGCTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACGAGAC
          1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACGACAC

                 
       5702 GTGCT
         62 GTGCT

                      
       5707 AAACAGAGAG
          1 AAACAGAGAG

       5717 CGCGCTAGTG


Statistics
Matches: 70,  Mismatches: 4, Indels: 10
        0.83            0.05        0.12

Matches are distributed among these distances:
  68    2  0.03
  69   38  0.54
  70   13  0.19
  71   11  0.16
  72    6  0.09

ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13


Consensus pattern (66 bp):   
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACGACACGTGC
T

Found at i:5706 original size:46 final size:45

Alignment explanation


    Indices: 5569--5717  Score: 126
    Period size: 46  Copynumber: 3.2  Consensus size: 45

       5559 TATACAAAAC

                      *         *                      *  
       5569 AAACAGAGAGTAC-CAAAGTACT-AACAGAGAG-CACATAAGTTCT
          1 AAACAGAGAGCACACAAAGTGCTAAACAGAGAGACACA-AAGTGCT

               *               **                            
       5612 GGGCAACAGAGAGCACACACTGTGCTAAACAGAGAGTACACAAAGTGCT
          1 ---AAACAGAGAGCACACAAAGTGCTAAACAGAGAG-ACACAAAGTGCT

              *                      *               *     
       5661 AATCAGAGAGCACACAAAGTGCTAATCAGAGAG-CACGAGACGTGCT
          1 AAACAGAGAGCACACAAAGTGCTAAACAGAGAGACAC-A-AAGTGCT

                       
       5707 AAACAGAGAGC
          1 AAACAGAGAGC

       5718 GCGCTAGTGT


Statistics
Matches: 84,  Mismatches: 13, Indels: 12
        0.77            0.12        0.11

Matches are distributed among these distances:
  44    3  0.04
  45    1  0.01
  46   55  0.65
  47    6  0.07
  48    9  0.11
  49    6  0.07
  50    4  0.05

ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13


Consensus pattern (45 bp):   
AAACAGAGAGCACACAAAGTGCTAAACAGAGAGACACAAAGTGCT
Done.