Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003327.1 Kokia drynarioides strain JFW-HI SEQ_116026, 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: 5819
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36


Found at i:3486 original size:33 final size:33

Alignment explanation


    Indices: 3443--3520  Score: 120
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       3433 GTTAAAAGAT

                 *                           
       3443 CAAATGGCTCAAATGCAAGCGAGCACAGTTGAG
          1 CAAATTGCTCAAATGCAAGCGAGCACAGTTGAG

                       *             *       
       3476 CAAATTGCTCAGATGCAAGCGAGCATAGTTGAG
          1 CAAATTGCTCAAATGCAAGCGAGCACAGTTGAG

                  *     
       3509 CAAATTACTCAA
          1 CAAATTGCTCAA

       3521 CTTAAAGCGA


Statistics
Matches: 40,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  33   40  1.00

ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19


Consensus pattern (33 bp):   
CAAATTGCTCAAATGCAAGCGAGCACAGTTGAG

Found at i:4044 original size:43 final size:43

Alignment explanation


    Indices: 3997--4173  Score: 175
    Period size: 43  Copynumber: 4.2  Consensus size: 43

       3987 ATCTGTTAAA

                                               *       
       3997 TTTAGCGGCGTTTGTGGGAAAAGCGTCGTTAAAGATCATGTTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGTCGTTAAAGACCATGTTC

                   * *                *                 
       4040 TTTAGCGACATTTGTGAGG-AAAGCGCCGTTAAAGACCATGTTC
          1 TTTAGCGGCGTTTGTG-GGAAAAGCGTCGTTAAAGACCATGTTC

                            *  *        *              
       4083 TTTA---GCGTTTGTGAGAGAAGCGTCGCTAAAGACCATGTTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGTCGTTAAAGACCATGTTC

                  *      *      *    *  *         **   
       4123 TTTAGCAGCGTTTATGGG-ATAGCGCCGCTAAAGACCACATTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGTCGTTAAAGACCATGTTC

             *       
       4165 TATAGCGGC
          1 TTTAGCGGC

       4174 ATTTTTCCTT


Statistics
Matches: 110,  Mismatches: 19, Indels: 11
        0.79            0.14        0.08

Matches are distributed among these distances:
  39    1  0.01
  40   32  0.29
  42   26  0.24
  43   49  0.45
  44    2  0.02

ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29


Consensus pattern (43 bp):   
TTTAGCGGCGTTTGTGGGAAAAGCGTCGTTAAAGACCATGTTC

Found at i:4113 original size:40 final size:40

Alignment explanation


    Indices: 4004--4128  Score: 162
    Period size: 40  Copynumber: 3.0  Consensus size: 40

       3994 AAATTTAGCG

                     *  *               *           
       4004 GCGTTTGTGGGAAAAGCGTCGTTAAAGATCATGTTCTTTA
          1 GCGTTTGTGAGAGAAGCGTCGTTAAAGACCATGTTCTTTA

                                  *                     
       4044 GCGACATTTGTGAG-GAAAGCGCCGTTAAAGACCATGTTCTTTA
          1 GCG---TTTGTGAGAG-AAGCGTCGTTAAAGACCATGTTCTTTA

                                 *                  
       4087 GCGTTTGTGAGAGAAGCGTCGCTAAAGACCATGTTCTTTA
          1 GCGTTTGTGAGAGAAGCGTCGTTAAAGACCATGTTCTTTA

              
       4127 GC
          1 GC

       4129 AGCGTTTATG


Statistics
Matches: 74,  Mismatches: 6, Indels: 10
        0.82            0.07        0.11

Matches are distributed among these distances:
  40   38  0.51
  41    1  0.01
  43   35  0.47

ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30


Consensus pattern (40 bp):   
GCGTTTGTGAGAGAAGCGTCGTTAAAGACCATGTTCTTTA

Found at i:4123 original size:83 final size:82

Alignment explanation


    Indices: 4004--4159  Score: 215
    Period size: 83  Copynumber: 1.9  Consensus size: 82

       3994 AAATTTAGCG

                     *           *      *                     *              
       4004 GCGTTTGTGGGAAAAGCGTCGTTAAAGATCATGTTCTTTAGC-GACATTTGTGAGGAAAGCGCCG
          1 GCGTTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTTTAGCAG-CATTTATG-GGAAAGCGCCG

            *                  
       4068 TTAAAGACCATGTTCTTTA
         64 CTAAAGACCATGTTCTTTA

                        *                                *         *         
       4087 GCGTTTGTGAGAGAAGCGTCGCTAAAGACCATGTTCTTTAGCAGCGTTTATGGGATAGCGCCGCT
          1 GCGTTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTTTAGCAGCATTTATGGGAAAGCGCCGCT

                    
       4152 AAAGACCA
         66 AAAGACCA

       4160 CATTCTATAG


Statistics
Matches: 64,  Mismatches: 8, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  82   19  0.30
  83   44  0.69
  84    1  0.02

ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28


Consensus pattern (82 bp):   
GCGTTTGTGAGAAAAGCGTCGCTAAAGACCATGTTCTTTAGCAGCATTTATGGGAAAGCGCCGCT
AAAGACCATGTTCTTTA
Done.