Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010102.1 Kokia drynarioides strain JFW-HI SEQ_124886, 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: 2761
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.35

Warning! 125 characters in sequence are not A, C, G, or T


Found at i:61 original size:17 final size:17

Alignment explanation


    Indices: 1--63  Score: 90
    Period size: 17  Copynumber: 3.7  Consensus size: 17

                     *    *  
          1 TAAATTTAATTTTATAA
          1 TAAATTTAAATTTAAAA

                         *   
         18 TAAATTTAAATTTCAAA
          1 TAAATTTAAATTTAAAA

                             
         35 TAAATTTAAATTTAAAA
          1 TAAATTTAAATTTAAAA

                *       
         52 TAAACTTAAATT
          1 TAAATTTAAATT

         64 CAATTTCCAA


Statistics
Matches: 41,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   41  1.00

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44


Consensus pattern (17 bp):   
TAAATTTAAATTTAAAA

Found at i:812 original size:139 final size:139

Alignment explanation


    Indices: 529--1042  Score: 736
    Period size: 139  Copynumber: 3.7  Consensus size: 139

        519 ATTCGCTTAT

                *             *   *       *       *      *   *              *
        529 GAATTTGGTTCACTTCTCAGTACCTCATCTTGGAAGATCTGCTCGCTTCAAGCCTCGTTTGGGTA
          1 GAATCTGGTTCACTTCTCCGTATCTCATC-AGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTT

             *        *        *                        *            *       
        594 TCCTTCTCAGCGTCTCATCGGGAAGATG----C-TCACTGTTTCAATCCGTTTCTCTATATCTCA
         65 TTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCA

             *       *
        654 TTAGGAAGAT
        130 TCAGGAAGAC

                                              *                              
        664 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAATATTTGCTC-TCTTCGAGCCTCGTTTGGGTT
          1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGT-TTCGAGCCTCGTTTGGGTT

                     *                          *         *                  
        728 TTCTTCTCAATGTCTCATCAGGAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCA
         65 TTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCA

                      
        793 TCAGGAAGAC
        130 TCAGGAAGAC

                                                                             
        803 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTT
          1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTT

                                                   *                       * 
        868 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGCTTCGATCCGTTTCTCTGTATCTCTT
         66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT

                      
        933 CAGG-AGTAC
        131 CAGGAAG-AC

                  *          *                                    *          
        942 GAATCTAGTTCACTTCTTCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
          1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTT

                                                
       1007 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCA
         66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCA

       1043 NNNNNNNNNN


Statistics
Matches: 343,  Mismatches: 28, Indels: 12
        0.90            0.07        0.03

Matches are distributed among these distances:
 134   52  0.15
 135   26  0.08
 138    3  0.01
 139  261  0.76
 140    1  0.00

ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36


Consensus pattern (139 bp):   
GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTT
TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
CAGGAAGAC
Done.