Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005057.1 Corchorus capsularis cultivar CVL-1 contig05075, 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: 18845
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32


Found at i:14363 original size:49 final size:45

Alignment explanation


    Indices: 14314--14402  Score: 160
    Period size: 45  Copynumber: 2.0  Consensus size: 45

      14304 TACATAACCA

                            *                            
      14314 ACCAATTCATACAACAGACAAACATACTTTTCCATTAGGGTTTCT
          1 ACCAATTCATACAACACACAAACATACTTTTCCATTAGGGTTTCT

                             *                          
      14359 ACCAATTCATACAACACCCAAACATACTTTTCCATTAGGGTTTC
          1 ACCAATTCATACAACACACAAACATACTTTTCCATTAGGGTTTC

      14403 CACATTTATG


Statistics
Matches: 42,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30


Consensus pattern (45 bp):   
ACCAATTCATACAACACACAAACATACTTTTCCATTAGGGTTTCT

Found at i:15549 original size:59 final size:59

Alignment explanation


    Indices: 15457--15574  Score: 200
    Period size: 59  Copynumber: 2.0  Consensus size: 59

      15447 GAATCCCCCC

                   *                                             *     
      15457 TCTAACTGAGTTAAGTTAGAGCTAAAGATTAGTTTCATCTGAGATATAGGTATTAGCAT
          1 TCTAACTAAGTTAAGTTAGAGCTAAAGATTAGTTTCATCTGAGATATAGGTATCAGCAT

                                                  *      *             
      15516 TCTAACTAAGTTAAGTTAGAGCTAAAGATTAGTTTCATTTGAGATTTAGGTATCAGCAT
          1 TCTAACTAAGTTAAGTTAGAGCTAAAGATTAGTTTCATCTGAGATATAGGTATCAGCAT

      15575 AGATTCCTTT


Statistics
Matches: 55,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  59   55  1.00

ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36


Consensus pattern (59 bp):   
TCTAACTAAGTTAAGTTAGAGCTAAAGATTAGTTTCATCTGAGATATAGGTATCAGCAT

Found at i:16732 original size:3 final size:3

Alignment explanation


    Indices: 16721--16755  Score: 63
    Period size: 3  Copynumber: 12.0  Consensus size: 3

      16711 AAAAAAAAGA

                                                           
      16721 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

      16756 CTTTTTGTAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2    2  0.06
   3   29  0.94

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (3 bp):   
AAG

Done.