Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013833.1 Corchorus capsularis cultivar CVL-1 contig13854, 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: 16425
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:3421 original size:25 final size:25

Alignment explanation


    Indices: 3392--3443  Score: 77
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       3382 CACCAGAAAT

                                     
       3392 AAAGAATACAAACCCTTGGATTAGG
          1 AAAGAATACAAACCCTTGGATTAGG

                    *     *    *     
       3417 AAAGAATATAAACCTTTGGGTTAGG
          1 AAAGAATACAAACCCTTGGATTAGG

              
       3442 AA
          1 AA

       3444 TGATCTCCAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23


Consensus pattern (25 bp):   
AAAGAATACAAACCCTTGGATTAGG

Found at i:7575 original size:23 final size:23

Alignment explanation


    Indices: 7521--7575  Score: 74
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       7511 TAAAATTATT

                             * *   
       7521 TAAACCTTACCCTAGTATTCTCC
          1 TAAACCTTACCCTAGTAATATCC

            *                      
       7544 AAAACCTTACCCTAGTAATATCC
          1 TAAACCTTACCCTAGTAATATCC

                *    
       7567 TAAATCTTA
          1 TAAACCTTA

       7576 GGACTTGCTT


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  23   27  1.00

ACGTcount: A:0.35, C:0.29, G:0.04, T:0.33


Consensus pattern (23 bp):   
TAAACCTTACCCTAGTAATATCC

Found at i:15872 original size:15 final size:16

Alignment explanation


    Indices: 15852--15890  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

      15842 GTTCAAATGA

                            
      15852 GGAGGGGTAGGG-TAG
          1 GGAGGGGTAGGGTTAG

                   *      * 
      15867 GGAGGGGGAGGGTTTG
          1 GGAGGGGTAGGGTTAG

                    
      15883 GGAGGGGT
          1 GGAGGGGT

      15891 TTTAGAAAAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  15   11  0.55
  16    9  0.45

ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15


Consensus pattern (16 bp):   
GGAGGGGTAGGGTTAG
Done.