Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013604.1 Kokia drynarioides strain JFW-HI SEQ_128631, 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: 7222
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34


Found at i:7074 original size:23 final size:23

Alignment explanation


    Indices: 7001--7174  Score: 131
    Period size: 23  Copynumber: 7.5  Consensus size: 23

       6991 TATACGGAAC

                      *     *   *  
       7001 AAACAGAGAGTAC-CAAAGTACT
          1 AAACAGAGAGCACACACAGTGCT

                          *        
       7023 -AACAGAGAGCACATA-AGTGCT
          1 AAACAGAGAGCACACACAGTGCT

               *             *        
       7044 GGGCAACAGAGAGCACATACAGTGCT
          1 ---AAACAGAGAGCACACACAGTGCT

                      *     *   *  
       7070 AAACAGAGAGTACACAAAGTACT
          1 AAACAGAGAGCACACACAGTGCT

              *             *      
       7093 AATCAGAGAGCACACAAAGTGCT
          1 AAACAGAGAGCACACACAGTGCT

              *       *            *
       7116 AATCAGAGAGAACACACAGTGCCA
          1 AAACAGAGAGCACACACAGTG-CT

                            *        
       7140 ATAACAGAGAGCACGAGAC-GTGCT
          1 A-AACAGAGAGCAC-ACACAGTGCT

                       
       7164 AAACAGAGAGC
          1 AAACAGAGAGC

       7175 GCGCTAGTGT


Statistics
Matches: 125,  Mismatches: 18, Indels: 17
        0.78            0.11        0.11

Matches are distributed among these distances:
  21   16  0.13
  22    1  0.01
  23   67  0.54
  24    4  0.03
  25   28  0.22
  26    9  0.07

ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11


Consensus pattern (23 bp):   
AAACAGAGAGCACACACAGTGCT

Found at i:7100 original size:46 final size:47

Alignment explanation


    Indices: 7049--7173  Score: 146
    Period size: 46  Copynumber: 2.7  Consensus size: 47

       7039 GTGCTGGGCA

                        *                  *           *   
       7049 ACAGAGAGCACATACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
          1 ACAGAGAGCACACACAGTGCTAAACAGAGAGAACACAAAGTACCAAT

                          *        *             *   *     
       7096 -CAGAGAGCACACAAAGTGCTAATCAGAGAGAACACACAGTGCCAAT
          1 ACAGAGAGCACACACAGTGCTAAACAGAGAGAACACAAAGTACCAAT

                          *                  
       7142 AACAGAGAGCACGAGAC-GTGCTAAACAGAGAG
          1 -ACAGAGAGCAC-ACACAGTGCTAAACAGAGAG

       7174 CGCGCTAGTG


Statistics
Matches: 65,  Mismatches: 10, Indels: 5
        0.81            0.12        0.06

Matches are distributed among these distances:
  46   39  0.60
  48   24  0.37
  49    2  0.03

ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11


Consensus pattern (47 bp):   
ACAGAGAGCACACACAGTGCTAAACAGAGAGAACACAAAGTACCAAT

Found at i:7123 original size:69 final size:66

Alignment explanation


    Indices: 7001--7137  Score: 177
    Period size: 69  Copynumber: 2.0  Consensus size: 66

       6991 TATACGGAAC

                                               *                    *   *    
       7001 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACATACAG
          1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGAACACACAG

                
       7066 TGCT
         63 TGCT

                                                                             
       7070 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGAACACACA
          1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGAACACACA

                
       7134 GTGC
         62 GTGC

       7138 CAATAACAGA


Statistics
Matches: 61,  Mismatches: 3, Indels: 8
        0.85            0.04        0.11

Matches are distributed among these distances:
  68    2  0.03
  69   30  0.49
  70   11  0.18
  71   11  0.18
  72    7  0.11

ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12


Consensus pattern (66 bp):   
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGAACACACAGTGC
T

Done.