Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004658.1 Kokia drynarioides strain JFW-HI SEQ_118198, 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: 29289
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:7535 original size:349 final size:349

Alignment explanation


    Indices: 6914--7572  Score: 953
    Period size: 349  Copynumber: 1.9  Consensus size: 349

       6904 GGACTGCTCT

                                        *      *                   *         
       6914 TGCACGAGTTACAAGTACTGCACATGAGTGTATTCGATTTAGTATTATGTTAGTAGGTGGCATAG
          1 TGCACGAGTTACAAGTACTGCACATGAGCGTATTCAATTTAGTATTATGTTAGTAAGTGGCATAG

                           *          *     *   *       **                   
       6979 TATTAGATTTTAATGTAAAGTTTATTGTCATAGGTCTTAATTCAGTTAGACCCAGAGTTAGATCT
         66 TATTAGATTTTAATGCAAAGTTTATTCTCATAAGTCCTAATTCAACTAGACCCAGAGTTAGATCT

                                         *       *       *                   
       7044 AACTATGAGAGGCGTCCTCCACGACGTTAGAGCTTCTGCCCACTAGAGGTGTGTTTCTTCATGTG
        131 AACTATGAGAGGCGTCCTCCACGACGTTAAAGCTTCTACCCACTAAAGGTGTGTTTCTTCATGTG

                                        *               *  *                 
       7109 CTACATTTTATTGTGTGACGATGTTCCATACCTTGTGTGATATTCTTCTGTGTTGTGATATTTAT
        196 CTACATTTTATTGTGTGACGATGTTCCACACCTTGTGTGATATTATTATGTGTTGTGATATTTAT

                                                                             
       7174 ATCATTTTATTCCGTGATGCGTATCACATGTTAATATTCCATACATATTAGGCTGACAAGTTACC
        261 ATCATTTTATTCCGTGATGCGTATCACATGTTAATATTCCATACATATTAGGCTGACAAGTTACC

                                    
       7239 TCCTTCACCTATGTTGACTACCCC
        326 TCCTTCACCTATGTTGACTACCCC

                        *   *                             *              *   
       7263 TGCACGAGTTACGAGTGCTGCACATGAGCGTATTCAATTTAGTATTGTGTTAGTAAGTGGCCTAG
          1 TGCACGAGTTACAAGTACTGCACATGAGCGTATTCAATTTAGTATTATGTTAGTAAGTGGCATAG

                              *                                **            
       7328 TGA-TAGATTTTAATGCAGAGTTTATTCTCATAAGTCCTAATTCAACTAGAGTC-GAAGTTAGAT
         66 T-ATTAGATTTTAATGCAAAGTTTATTCTCATAAGTCCTAATTCAACTAGACCCAG-AGTTAGAT

                * *             *  *   *         *     *                  *  
       7391 CTAAGTGTGAGAGGCGTCCTTCATGACTTTAAAGCTTTTACCCGCTAAAGGTGTGTTTCTTCCTG
        129 CTAACTATGAGAGGCGTCCTCCACGACGTTAAAGCTTCTACCCACTAAAGGTGTGTTTCTTCATG

                       *          *                                          
       7456 TGCTACATTTTGTTGTGTGACGGTGTTCCACACCTTGTGTGATATTATTATGTGTTGTGATATTT
        194 TGCTACATTTTATTGTGTGACGATGTTCCACACCTTGTGTGATATTATTATGTGTTGTGATATTT

            *                          *      *      *  *       
       7521 GTATCATTTTATTCCGTGATGCGTATCGCATGTTGATATTCTATTCATATTA
        259 ATATCATTTTATTCCGTGATGCGTATCACATGTTAATATTCCATACATATTA

       7573 TTAGACTGTG


Statistics
Matches: 271,  Mismatches: 37, Indels: 4
        0.87            0.12        0.01

Matches are distributed among these distances:
 348    1  0.00
 349  269  0.99
 350    1  0.00

ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39


Consensus pattern (349 bp):   
TGCACGAGTTACAAGTACTGCACATGAGCGTATTCAATTTAGTATTATGTTAGTAAGTGGCATAG
TATTAGATTTTAATGCAAAGTTTATTCTCATAAGTCCTAATTCAACTAGACCCAGAGTTAGATCT
AACTATGAGAGGCGTCCTCCACGACGTTAAAGCTTCTACCCACTAAAGGTGTGTTTCTTCATGTG
CTACATTTTATTGTGTGACGATGTTCCACACCTTGTGTGATATTATTATGTGTTGTGATATTTAT
ATCATTTTATTCCGTGATGCGTATCACATGTTAATATTCCATACATATTAGGCTGACAAGTTACC
TCCTTCACCTATGTTGACTACCCC

Found at i:10101 original size:30 final size:30

Alignment explanation


    Indices: 10027--10129  Score: 84
    Period size: 30  Copynumber: 3.4  Consensus size: 30

      10017 CCCAAAATTT

                    *       *         *    
      10027 ATTTAAGGATTAAATTGGAAATTTT-GTAAA
          1 ATTTAAGGGTT-AATTTGAAATTTTAATAAA

                      *       *            
      10057 ATTT-AGGGACTAATTTGTAATTTTAATAAA
          1 ATTTAAGGG-TTAATTTGAAATTTTAATAAA

                            *  *     *    
      10087 ATTTAAGGGTTAATTTCAACTTTTATTAAA
          1 ATTTAAGGGTTAATTTGAAATTTTAATAAA

                * *      
      10117 ATTTGATGGTTAA
          1 ATTTAAGGGTTAA

      10130 GTTGGATTTT


Statistics
Matches: 58,  Mismatches: 12, Indels: 6
        0.76            0.16        0.08

Matches are distributed among these distances:
  29   14  0.24
  30   40  0.69
  31    4  0.07

ACGTcount: A:0.39, C:0.03, G:0.15, T:0.44


Consensus pattern (30 bp):   
ATTTAAGGGTTAATTTGAAATTTTAATAAA

Found at i:12759 original size:24 final size:24

Alignment explanation


    Indices: 12727--12783  Score: 96
    Period size: 24  Copynumber: 2.4  Consensus size: 24

      12717 AAAGATTGAT

                         *          
      12727 GTAGGATATACCATAATCCATGTA
          1 GTAGGATATACCACAATCCATGTA

              *                     
      12751 GTTGGATATACCACAATCCATGTA
          1 GTAGGATATACCACAATCCATGTA

                     
      12775 GTAGGATAT
          1 GTAGGATAT

      12784 GTAGTGGGAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   30  1.00

ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30


Consensus pattern (24 bp):   
GTAGGATATACCACAATCCATGTA

Found at i:14152 original size:16 final size:17

Alignment explanation


    Indices: 14128--14160  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      14118 TCTCTTCTTC

                             
      14128 TTCTCC-TTTTCTTTTA
          1 TTCTCCTTTTTCTTTTA

                *            
      14144 TTCTTCTTTTTCTTTTA
          1 TTCTCCTTTTTCTTTTA

      14161 CTGCCTAATC


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73


Consensus pattern (17 bp):   
TTCTCCTTTTTCTTTTA
Done.