Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009189.1 Kokia drynarioides strain JFW-HI SEQ_123894, 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: 15640
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35


Found at i:82 original size:17 final size:17

Alignment explanation


    Indices: 62--106  Score: 72
    Period size: 17  Copynumber: 2.6  Consensus size: 17

         52 CAAATCTATG

                             
         62 ATAAATTTAAATTTAAA
          1 ATAAATTTAAATTTAAA

                 *    *      
         79 ATAAACTTAATTTTAAA
          1 ATAAATTTAAATTTAAA

                       
         96 ATAAATTTAAA
          1 ATAAATTTAAA

        107 GTCTGTCGGG


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  17   24  1.00

ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40


Consensus pattern (17 bp):   
ATAAATTTAAATTTAAA

Found at i:10809 original size:7 final size:7

Alignment explanation


    Indices: 10797--10821  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

      10787 GAGTCATCCA

                   
      10797 TTTTATT
          1 TTTTATT

                   
      10804 TTTTATT
          1 TTTTATT

                   
      10811 TTTTATT
          1 TTTTATT

                
      10818 TTTT
          1 TTTT

      10822 TTTAATTATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88


Consensus pattern (7 bp):   
TTTTATT

Found at i:13053 original size:161 final size:162

Alignment explanation


    Indices: 12667--13086  Score: 460
    Period size: 161  Copynumber: 2.6  Consensus size: 162

      12657 AACAATTGAG

                   *              *          *                               
      12667 CTAGTAAACCAATTGTTTCATTCGTAGAAACTACAATATATGAAGCTTTTCTCTATTGGTTAAAT
          1 CTAGTAAGCCAATTGTTTCATTTGTAGAAACTATAATATATGAAGCTTTTCTC-ATTGGTTAAAT

                *   *                                       *        *       
      12732 GATACTAAGTTATTCGGCCTAAGATAAACAATAATAATAACTTATTCAGCCCATTGTTCTACGAC
         65 GATAATAAATTATTCGGCCTAAGATAAACAATAATAAT-A-TTATTCAACCC--TGTCCTACGAC

                             * *            *  **
      12797 CTTCATGTTAATAGCACGAGGCTACAACCAAGTAAGT
        126 CTTCATGTTAATAGCACAAAGCTACAACCAAGCAACA

                       *  *                               *                  
      12834 C-AGTAAGCCAGTTATTTCATTTGTAGGAAA-TATAATATATGAAGTTTTTCTCCATTGGTTAAA
          1 CTAGTAAGCCAATTGTTTCATTTGTA-GAAACTATAATATATGAAGCTTTTCT-CATTGGTTAAA

                      *                                                     *
      12897 TGATAATAAACTATTCGGCCTAAGA-AATA-AATAATAAT-TTATTCAACCC-GTACCTACGA-T
         64 TGATAATAAATTATTCGGCCTAAGATAA-ACAATAATAATATTATTCAACCCTGT-CCTACGACC

               *       *     *          *         
      12957 TATTAGTGTTAGTAGCATAAAGCTACAATC-AGCAACA
        127 T-TCA-TGTTAATAGCACAAAGCTACAACCAAGCAACA

                                                  *         *                
      12994 CTAGTAAGCCAATTGTTTCATTTGTAGAAACTATAATACATGAAGCTTGTCTGCATTGGTTAAAT
          1 CTAGTAAGCCAATTGTTTCATTTGTAGAAACTATAATATATGAAGCTTTTCT-CATTGGTTAAAT

                             *          
      13059 GATAATAAATTATTCGGTCTAAGATAAA
         65 GATAATAAATTATTCGGCCTAAGATAAA

      13087 ATAGTAACTT


Statistics
Matches: 215,  Mismatches: 29, Indels: 24
        0.80            0.11        0.09

Matches are distributed among these distances:
 159    3  0.01
 160   17  0.08
 161   94  0.44
 162   12  0.06
 165   11  0.05
 166   72  0.33
 167    6  0.03

ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33


Consensus pattern (162 bp):   
CTAGTAAGCCAATTGTTTCATTTGTAGAAACTATAATATATGAAGCTTTTCTCATTGGTTAAATG
ATAATAAATTATTCGGCCTAAGATAAACAATAATAATATTATTCAACCCTGTCCTACGACCTTCA
TGTTAATAGCACAAAGCTACAACCAAGCAACA
Done.