Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010913.1 Kokia drynarioides strain JFW-HI SEQ_125881, 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: 14505
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:146 original size:23 final size:23

Alignment explanation


    Indices: 95--212  Score: 130
    Period size: 23  Copynumber: 5.0  Consensus size: 23

         85 TCTAAGTATT

                          *        
         95 AACAGAGAGCACA-TAAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

                              *       
        117 GGCAACAGAGAGCACACACAGTGCTA
          1 ---AACAGAGAGCACACAAAGTGCTA

                     *         *   
        143 AACAGAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACAAAGTGCTA

             *         *           
        166 ATCAGAGAGCATACAAAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

             *             *       
        189 ATCAGAGAGCACACACAGTGCTA
          1 AACAGAGAGCACACAAAGTGCTA

             
        212 A
          1 A

        213 TAACAAAGAG


Statistics
Matches: 81,  Mismatches: 11, Indels: 4
        0.84            0.11        0.04

Matches are distributed among these distances:
  23   61  0.75
  25   13  0.16
  26    7  0.09

ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13


Consensus pattern (23 bp):   
AACAGAGAGCACACAAAGTGCTA

Found at i:7288 original size:46 final size:46

Alignment explanation


    Indices: 7186--7290  Score: 165
    Period size: 47  Copynumber: 2.3  Consensus size: 46

       7176 ATCGGTTCGG

                           *                          ** *
       7186 TTTTTAGAATTGTTCGTCATAATTCGATTCTTAATTTTTTTTTTTT
          1 TTTTTAGAATTGTTCATCATAATTCGATTCTTAATTTTTTTTCGTA

                                                           
       7232 TGTTTTAGAATTGTTCATCATAATTCGATTCTTAATTTTTTTTCGTA
          1 T-TTTTAGAATTGTTCATCATAATTCGATTCTTAATTTTTTTTCGTA

                        
       7279 TTTTTAGAATTG
          1 TTTTTAGAATTG

       7291 ACAAAATGAG


Statistics
Matches: 54,  Mismatches: 4, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  46   12  0.22
  47   42  0.78

ACGTcount: A:0.22, C:0.09, G:0.10, T:0.59


Consensus pattern (46 bp):   
TTTTTAGAATTGTTCATCATAATTCGATTCTTAATTTTTTTTCGTA

Found at i:9955 original size:13 final size:13

Alignment explanation


    Indices: 9937--9962  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       9927 TTTCTGTATT

                         
       9937 TTAAAATAAATAA
          1 TTAAAATAAATAA

                         
       9950 TTAAAATAAATAA
          1 TTAAAATAAATAA

       9963 AAACATATGT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (13 bp):   
TTAAAATAAATAA

Found at i:13491 original size:23 final size:23

Alignment explanation


    Indices: 13465--13614  Score: 158
    Period size: 23  Copynumber: 6.4  Consensus size: 23

      13455 AGTGCTGGGC

                                   
      13465 AACAGAGAGCACACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

                     *     *   *   
      13488 AACAGAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

             *    *        *       
      13511 ATCAGAAAGCACACAAAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

             *                      
      13534 ATCAGAGAGCACACACAGTGCTAA
          1 AACAGAGAGCACACACAGTGCT-A

                         * *     *   
      13558 TAACAGAGAGCATGAGAC-GTACTA
          1 -AACAGAGAGCA-CACACAGTGCTA

                       *           
      13582 AACAGAGAGCATACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

             *        
      13605 ATCAGAGAGC
          1 AACAGAGAGC

      13615 GCGCTAGTGT


Statistics
Matches: 106,  Mismatches: 17, Indels: 8
        0.81            0.13        0.06

Matches are distributed among these distances:
  22    3  0.03
  23   84  0.79
  24    2  0.02
  25   14  0.13
  26    3  0.03

ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13


Consensus pattern (23 bp):   
AACAGAGAGCACACACAGTGCTA

Found at i:13580 original size:71 final size:68

Alignment explanation


    Indices: 13467--13614  Score: 190
    Period size: 71  Copynumber: 2.1  Consensus size: 68

      13457 TGCTGGGCAA

                                                         *                   
      13467 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAATCAGAAAGCACACAAAGTGC
          1 CAGAGAGCACACACAGTGCTAAACAGAGAG-ACACAAAGTACTAAACAGAAAGCACACAAAGTGC

                
      13532 TAAT
         65 TAAT

                                                *   *            *    *   *  
      13536 CAGAGAGCACACACAGTGCTAATAACAGAGAG-CATGAGACGTACTAAACAGAGAGCATACACAG
          1 CAGAGAGCACACACAGTGCT-A-AACAGAGAGACA-CA-AAGTACTAAACAGAAAGCACACAAAG

                   
      13600 TGCTAAT
         62 TGCTAAT

                    
      13607 CAGAGAGC
          1 CAGAGAGC

      13615 GCGCTAGTGT


Statistics
Matches: 69,  Mismatches: 6, Indels: 6
        0.85            0.07        0.07

Matches are distributed among these distances:
  69   22  0.32
  70    2  0.03
  71   45  0.65

ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13


Consensus pattern (68 bp):   
CAGAGAGCACACACAGTGCTAAACAGAGAGACACAAAGTACTAAACAGAAAGCACACAAAGTGCT
AAT
Done.