Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011466.1 Kokia drynarioides strain JFW-HI SEQ_126450, 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: 9286
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24

Warning! 30 characters in sequence are not A, C, G, or T


Found at i:7035 original size:201 final size:201

Alignment explanation


    Indices: 6678--7316  Score: 1046
    Period size: 201  Copynumber: 3.2  Consensus size: 201

       6668 TACGATACCC

                 *                 *        *      * *                    *  
       6678 ACAAATGATGCAGTCATCTTCCTAATGAGACATCGAGAATATGACCCAAACAAGGCTCAAAGTGA
          1 ACAAACGATGCAGTCATCTTCCTGATGAGACACCGAGAAGAAGACCCAAACAAGGCTCAAAGCGA

             *              *                                                
       6743 GAGAAATCTTCAAAACTTAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTT
         66 GCGAAATCTTCAAAACCTAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTT

                                                                          *  
       6808 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGATATACAGAGAAGTGA
        131 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGATATACAGAGAAGCGA

                  
       6873 GTTGAA
        196 GTTGAA

                  *    *                                       *             
       6879 ACAAACAATGCGGTCATCTTCCTGATGAGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGCGA
          1 ACAAACGATGCAGTCATCTTCCTGATGAGACACCGAGAAGAAGACCCAAACAAGGCTCAAAGCGA

                             * *                                             
       6944 GCGAAATCTTCAAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTT
         66 GCGAAATCTTCAAAACCTAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTT

                                                                             
       7009 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGATATACAGAGAAGCGA
        131 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGATATACAGAGAAGCGA

                  
       7074 GTTGAA
        196 GTTGAA

                                                                             
       7080 ACAAACGATGCAGTCATCTTCCTGATGAGACACCGAGAAGAAGACCCAAACAAGGCTCAAAGCGA
          1 ACAAACGATGCAGTCATCTTCCTGATGAGACACCGAGAAGAAGACCCAAACAAGGCTCAAAGCGA

                                  *                                          
       7145 GCGAAATCTTCAAAACCTAGCTACCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTT
         66 GCGAAATCTTCAAAACCTAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTT

                                    *    *     *              *              
       7210 AGCTTCCTGATGAGATACTGAGAAATGAAACAAATCCGTCTTCCTGATGAGATACAGAGAAGCGG
        131 AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGATATACAGAGAAGC-G

             *     
       7275 ATTTGAA
        195 AGTTGAA

                *      *                   *    
       7282 ACAAGCGATGCGGTCAT-TCTCCTGATGAGATACCG
          1 ACAAACGATGCAGTCATCT-TCCTGATGAGACACCG

       7317 CCGAGTCAAG


Statistics
Matches: 408,  Mismatches: 28, Indels: 3
        0.93            0.06        0.01

Matches are distributed among these distances:
 201  371  0.91
 202   37  0.09

ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21


Consensus pattern (201 bp):   
ACAAACGATGCAGTCATCTTCCTGATGAGACACCGAGAAGAAGACCCAAACAAGGCTCAAAGCGA
GCGAAATCTTCAAAACCTAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTT
AGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGATATACAGAGAAGCGA
GTTGAA

Found at i:7682 original size:17 final size:17

Alignment explanation


    Indices: 7654--7714  Score: 70
    Period size: 17  Copynumber: 3.5  Consensus size: 17

       7644 ATTTGTTTAA

                              
       7654 AATTTAAAATTTATTTTT
          1 AATTT-AAATTTATTTTT

                         *   
       7672 AATTTAAATTTA-ATTT
          1 AATTTAAATTTATTTTT

                              *
       7688 AAGTTTAAATTTATTTTCA
          1 AA-TTTAAATTTATTTT-T

                    
       7707 AATTTAAA
          1 AATTTAAA

       7715 ATTGCTAAGT


Statistics
Matches: 37,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
  16    5  0.14
  17   17  0.46
  18   13  0.35
  19    2  0.05

ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54


Consensus pattern (17 bp):   
AATTTAAATTTATTTTT

Found at i:8437 original size:16 final size:18

Alignment explanation


    Indices: 8416--8452  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       8406 AGTGATAAGT

                              
       8416 ATTAAT-AG-TAATATTA
          1 ATTAATCAGATAATATTA

                               
       8432 ATTAATCAGAATAATATTA
          1 ATTAATCAG-ATAATATTA

              
       8451 AT
          1 AT

       8453 AATGGACAAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  16    6  0.33
  17    2  0.11
  19   10  0.56

ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41


Consensus pattern (18 bp):   
ATTAATCAGATAATATTA

Found at i:8998 original size:35 final size:35

Alignment explanation


    Indices: 8952--9029  Score: 111
    Period size: 35  Copynumber: 2.2  Consensus size: 35

       8942 GACGGGGTCT

                             *   *     *       
       8952 CGACGGCCCACCGGAGATACCTAGGGGGCGACGCG
          1 CGACGGCCCACCGGAGAAACCCAGGGGACGACGCG

                                           *   
       8987 CGACGGCCCACCGGAGAAACCCAGGGGACGATGCG
          1 CGACGGCCCACCGGAGAAACCCAGGGGACGACGCG

               *    
       9022 CGATGGCC
          1 CGACGGCC

       9030 ACGNNNNNNN


Statistics
Matches: 38,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  35   38  1.00

ACGTcount: A:0.22, C:0.35, G:0.38, T:0.05


Consensus pattern (35 bp):   
CGACGGCCCACCGGAGAAACCCAGGGGACGACGCG
Done.