Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015222.1 Corchorus capsularis cultivar CVL-1 contig15243, 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: 10827
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--31  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

                                                          
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         32 CAATTGGCCT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:7531 original size:17 final size:17

Alignment explanation


    Indices: 7506--7540  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       7496 TGCATAATGT

                             
       7506 TAATATGCCAACAAGAA
          1 TAATATGCCAACAAGAA

                *     *      
       7523 TAATGTGCCACCAAGAA
          1 TAATATGCCAACAAGAA

             
       7540 T
          1 T

       7541 GACACTTTTT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20


Consensus pattern (17 bp):   
TAATATGCCAACAAGAA

Found at i:8379 original size:27 final size:27

Alignment explanation


    Indices: 8348--8518  Score: 288
    Period size: 27  Copynumber: 6.3  Consensus size: 27

       8338 CCACCATAGG

                                     * 
       8348 CGAAGTGGGAGGATCCACTGCTGGGAT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

            *                          
       8375 AGAAGTGGGAGGATCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                  **                   
       8402 CGAAGTAAGAGGATCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                                       
       8429 CGAAGTGGGAGGATCCACTGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                             *         
       8456 CGAAGTGGGAGGATCCAATGCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                               *       
       8483 CGAAGTGGGAGGATCCACTTCTGGGGT
          1 CGAAGTGGGAGGATCCACTGCTGGGGT

                     
       8510 CGAAGTGGG
          1 CGAAGTGGG

       8519 GAGAGAAGAC


Statistics
Matches: 134,  Mismatches: 10, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27  134  1.00

ACGTcount: A:0.22, C:0.17, G:0.43, T:0.19


Consensus pattern (27 bp):   
CGAAGTGGGAGGATCCACTGCTGGGGT

Found at i:9111 original size:66 final size:66

Alignment explanation


    Indices: 9005--9136  Score: 264
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       8995 GTTTTTAATG

                                                                             
       9005 CAACCAATTTAGATTAGATTAGATTAGCATAGCATTTTGTAGGTCTATATATAATTCATGCACAT
          1 CAACCAATTTAGATTAGATTAGATTAGCATAGCATTTTGTAGGTCTATATATAATTCATGCACAT

             
       9070 T
         66 T

                                                                             
       9071 CAACCAATTTAGATTAGATTAGATTAGCATAGCATTTTGTAGGTCTATATATAATTCATGCACAT
          1 CAACCAATTTAGATTAGATTAGATTAGCATAGCATTTTGTAGGTCTATATATAATTCATGCACAT

             
       9136 T
         66 T

       9137 TAGAATAAAG


Statistics
Matches: 66,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  66   66  1.00

ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38


Consensus pattern (66 bp):   
CAACCAATTTAGATTAGATTAGATTAGCATAGCATTTTGTAGGTCTATATATAATTCATGCACAT
T
Done.