Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012231.1 Kokia drynarioides strain JFW-HI SEQ_127232, 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: 3755
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:1775 original size:6 final size:6

Alignment explanation


    Indices: 1751--1814  Score: 71
    Period size: 6  Copynumber: 11.0  Consensus size: 6

       1741 TAATGGACTT

                 *        * *                                       
       1751 TTTAAT TTTAAA ATCAAA TTTAAA TTTAAA -TTAAA TTTAAA TTTAAGA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A

                                
       1799 -TT-AA TTTAAA TTTAAA
          1 TTTAAA TTTAAA TTTAAA

       1815 ATAAATTAAA


Statistics
Matches: 49,  Mismatches: 5, Indels: 8
        0.79            0.08        0.13

Matches are distributed among these distances:
   4    1  0.02
   5    8  0.16
   6   39  0.80
   7    1  0.02

ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47


Consensus pattern (6 bp):   
TTTAAA

Found at i:1784 original size:11 final size:11

Alignment explanation


    Indices: 1770--1821  Score: 61
    Period size: 11  Copynumber: 4.6  Consensus size: 11

       1760 AAAATCAAAT

                       
       1770 TTAAATTTAAA
          1 TTAAATTTAAA

                       
       1781 TTAAATTTAAA
          1 TTAAATTTAAA

                        *
       1792 TTTAAGA-TTAAT
          1 -TTAA-ATTTAAA

                       
       1804 TTAAATTTAAA
          1 TTAAATTTAAA

            *      
       1815 ATAAATT
          1 TTAAATT

       1822 AAAAGGGGGC


Statistics
Matches: 35,  Mismatches: 3, Indels: 6
        0.80            0.07        0.14

Matches are distributed among these distances:
  10    1  0.03
  11   25  0.71
  12    8  0.23
  13    1  0.03

ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46


Consensus pattern (11 bp):   
TTAAATTTAAA

Found at i:1786 original size:17 final size:17

Alignment explanation


    Indices: 1751--1821  Score: 90
    Period size: 17  Copynumber: 4.1  Consensus size: 17

       1741 TAATGGACTT

                 *        *   
       1751 TTTAATTTTAAAATCAAA
          1 TTTAAATTT-AAATTAAA

                             
       1769 TTTAAATTTAAATTAAA
          1 TTTAAATTTAAATTAAA

                              
       1786 TTTAAATTTAAGATT-AA
          1 TTTAAATTTAA-ATTAAA

                        *    
       1803 TTTAAATTTAAAATAAA
          1 TTTAAATTTAAATTAAA

              
       1820 TT
          1 TT

       1822 AAAAGGGGGC


Statistics
Matches: 48,  Mismatches: 3, Indels: 5
        0.86            0.05        0.09

Matches are distributed among these distances:
  16    2  0.04
  17   35  0.73
  18   11  0.23

ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46


Consensus pattern (17 bp):   
TTTAAATTTAAATTAAA

Found at i:2499 original size:206 final size:206

Alignment explanation


    Indices: 2140--2732  Score: 855
    Period size: 206  Copynumber: 2.9  Consensus size: 206

       2130 TTGACTTGAC

                                       *    **           **   **         * * 
       2140 CTTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTGTTTTGATCTACTTCTCTATGTTT
          1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCT

                     * * **                     *     *           *          
       2205 CATCAGGAACATGGCTTTGGTTCACTTCCTCA-TATTTCATCGGGAAGCTAACCGTTTTATTACT
         66 CATCAGGAAGACGAATTTGGTTCACTT-CTCAGTATCTCATCAGGAAGCTAACCATTTTATTACT

                                     *                           *     *     
       2269 TCGACCTGCTTCTCAGTATCTCATCGGGAAGCTGGGGTTCGAAGATTTGCTCATATCGAGCGTGG
        130 TCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAACGTGG

                        
       2334 GTTTGATTTGGT
        195 GTTTGATTTGGT

                                              * ***                  * *     
       2346 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAATCCGCTTCTTTGTATCT
          1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCT

                                                                 *       *   
       2411 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTT
         66 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT

                            *                 *            *                 
       2476 CGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGAGTTCGAAGATTTACTCACATCGAACGTGGG
        131 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAACGTGGG

                *      
       2541 TTTGGTTTGGT
        196 TTTGATTTGGT

                                                                             
       2552 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCT
          1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCT

                                                   *                         
       2617 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCAGCAGGAAGCTAACCATTTTATTACTT
         66 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT

                      *   *                 *                  
       2682 CGACCTGCTTATCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTC
        131 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC

       2733 GTTTTGAGCC


Statistics
Matches: 341,  Mismatches: 45, Indels: 2
        0.88            0.12        0.01

Matches are distributed among these distances:
 205    4  0.01
 206  337  0.99

ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35


Consensus pattern (206 bp):   
CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATATCT
CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTT
CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAACGTGGG
TTTGATTTGGT
Done.