Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006748.1 Kokia drynarioides strain JFW-HI SEQ_121346, 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: 9627
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:356 original size:91 final size:89

Alignment explanation


    Indices: 182--357  Score: 192
    Period size: 91  Copynumber: 2.0  Consensus size: 89

        172 ACACTCTAGT

                               * *                        *    *             
        182 TTGTGGATAAACCACAGTGTTGTAAGGTAATACGCTGCCAATAGTTGTGAATACACAACGAGTTT
          1 TTGTGGATAAACCACAGTGCTCTAAGGTAATACGCTGCCAATAGTTATGAACACACAACGAGTTT

             * *    *    *          
        247 GTAGATAATAGTCGCCAGTATAAG
         66 GCAAATAACAGTCACCAGTATAAG

                           *        *                 *                 * *  
        271 TTGTGGATAAACCAAGAGTGCTCTTAGGTTAATACGCTGCCAGTAGTTATGAACACACAATGGGT
          1 TTGTGGATAAACC-ACAGTGCTCTAAGG-TAATACGCTGCCAATAGTTATGAACACACAACGAGT

                    *              
        336 TTGCAAATTACAG-CTACCAGTA
         64 TTGCAAATAACAGTC-ACCAGTA

        358 ATTTATGGAT


Statistics
Matches: 70,  Mismatches: 14, Indels: 4
        0.80            0.16        0.05

Matches are distributed among these distances:
  89   13  0.19
  90   11  0.16
  91   46  0.66

ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28


Consensus pattern (89 bp):   
TTGTGGATAAACCACAGTGCTCTAAGGTAATACGCTGCCAATAGTTATGAACACACAACGAGTTT
GCAAATAACAGTCACCAGTATAAG

Found at i:6343 original size:67 final size:67

Alignment explanation


    Indices: 6205--6349  Score: 157
    Period size: 67  Copynumber: 2.2  Consensus size: 67

       6195 GGGAAGACCT

                  *     *          *       *  *               *    **   *    
       6205 AACTTTCCAACATCAACATGATGTGAAAAACTTTTGCAACTTCAACATGGTGAGAGGACCCATTT
          1 AACTTTGCAACACCAACATGATGGGAAAAACCTTCGCAACTTCAACATGGAGAGAAAACCAATTT

             *
       6270 CG
         66 CA

                                       *        *                      *     
       6272 AACTTTGCAACACCAACATGATGGGAAGAACCTTCGTAACTTCAACATGGAGAGAAAACTAA-TT
          1 AACTTTGCAACACCAACATGATGGGAAAAACCTTCGCAACTTCAACATGGAGAGAAAACCAATTT

               
       6336 CTA
         66 C-A

                       
       6339 AACTTTGCAAC
          1 AACTTTGCAAC

       6350 TTGAACATGA


Statistics
Matches: 64,  Mismatches: 13, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  66    3  0.05
  67   61  0.95

ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25


Consensus pattern (67 bp):   
AACTTTGCAACACCAACATGATGGGAAAAACCTTCGCAACTTCAACATGGAGAGAAAACCAATTT
CA

Found at i:8906 original size:17 final size:17

Alignment explanation


    Indices: 8886--8924  Score: 60
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       8876 ACTACAGTGC

                             
       8886 AAATGTACTAACAAATA
          1 AAATGTACTAACAAATA

                   * *       
       8903 AAATGTAGTGACAAATA
          1 AAATGTACTAACAAATA

                 
       8920 AAATG
          1 AAATG

       8925 CAATGACAAG


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.56, C:0.08, G:0.13, T:0.23


Consensus pattern (17 bp):   
AAATGTACTAACAAATA

Found at i:8931 original size:17 final size:17

Alignment explanation


    Indices: 8896--8938  Score: 59
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       8886 AAATGTACTA

                        * *  
       8896 ACAAATAAAATGTAGTG
          1 ACAAATAAAATGCAATG

                             
       8913 ACAAATAAAATGCAATG
          1 ACAAATAAAATGCAATG

                *    
       8930 ACAAGTAAA
          1 ACAAATAAA

       8939 TGATATGCAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   23  1.00

ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19


Consensus pattern (17 bp):   
ACAAATAAAATGCAATG
Done.