Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006778.1 Corchorus capsularis cultivar CVL-1 contig06799, 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: 20340
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:5596 original size:16 final size:16

Alignment explanation


    Indices: 5575--5605  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       5565 ATATATTAAT

                            
       5575 AAGTAAGATAAAAAAA
          1 AAGTAAGATAAAAAAA

                           
       5591 AAGTAAGATAAAAAA
          1 AAGTAAGATAAAAAA

       5606 GAAAATAATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13


Consensus pattern (16 bp):   
AAGTAAGATAAAAAAA

Found at i:6724 original size:112 final size:111

Alignment explanation


    Indices: 6497--6725  Score: 302
    Period size: 113  Copynumber: 2.0  Consensus size: 111

       6487 TTCTCAACCG

                       *                                             *     * 
       6497 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCCCGGATTATTGATGAGCTGGAGAAGT
          1 ACTTTAATAGAATAGTGGAATTACTAAAAGATCCCTACCCCGGATTATTGA-GAGCTAGAGAACT

                                                           
       6562 AATATTTTTCGTCTTTACCTACCTGGCAGATTACTTAAATGTCCTAA
         65 AATATTTTTCGTCTTTACCTACCTGGCAGATTACTTAAATGTCCTAA

                                                         * *          *      
       6609 ACTTTAATAGAATAGTGGAATTACTAAAAGATCCCTACCAAGCCTTGCTT-TTG-GAGTTAGAGA
          1 ACTTTAATAGAATAGTGGAATTACTAAAAGATCCCTACC---CC-GGATTATTGAGAGCTAGAGA

               *  *            *     *                        
       6672 ACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCT-A
         62 ACTAATATTTTTCGTCTTTACCTACCTGGCAGATTACTTAAATGTCCTAA

                 
       6721 ACTTT
          1 ACTTT

       6726 TGATTCTTTA


Statistics
Matches: 103,  Mismatches: 10, Indels: 8
        0.85            0.08        0.07

Matches are distributed among these distances:
 112   44  0.43
 113   51  0.50
 115    5  0.05
 116    3  0.03

ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36


Consensus pattern (111 bp):   
ACTTTAATAGAATAGTGGAATTACTAAAAGATCCCTACCCCGGATTATTGAGAGCTAGAGAACTA
ATATTTTTCGTCTTTACCTACCTGGCAGATTACTTAAATGTCCTAA
Done.