Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011067.1 Corchorus capsularis cultivar CVL-1 contig11088, 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: 35139
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:2540 original size:4 final size:4

Alignment explanation


    Indices: 2525--2568  Score: 51
    Period size: 4  Copynumber: 11.8  Consensus size: 4

       2515 AAGGTGAAGC

                                                                       
       2525 TTTA TATTA TTTA TTTA TTTA TTTA -TTA -TTA -TTA TTT- TTTA TTT
          1 TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT

       2569 TTTTTGCAAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   3   12  0.32
   4   21  0.57
   5    4  0.11

ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75


Consensus pattern (4 bp):   
TTTA

Found at i:10802 original size:2 final size:2

Alignment explanation


    Indices: 10795--10824  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      10785 ATCAGGAATT

                                        *               
      10795 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      10825 ATGAAATAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:14002 original size:113 final size:113

Alignment explanation


    Indices: 13804--14031  Score: 413
    Period size: 113  Copynumber: 2.0  Consensus size: 113

      13794 TAAGAAAACT

                                                                             
      13804 TGATATGAATATTTCCCAGCAGTAATACACAGAAAACCTTTTGCTCTATACAGCATAGCAAGCAC
          1 TGATATGAATATTTCCCAGCAGTAATACACAGAAAACCTTTTGCTCTATACAGCATAGCAAGCAC

                                                            
      13869 CGAAAAGCACATATCATGACAATTTCCTATCCCAATTCGGCCAATGTC
         66 CGAAAAGCACATATCATGACAATTTCCTATCCCAATTCGGCCAATGTC

                                                                      *    * 
      13917 TGATATGAATATTTCCCAGCAGTAATACACAGAAAACCTTTTGCTCTATACAGCATAGTAAGCTC
          1 TGATATGAATATTTCCCAGCAGTAATACACAGAAAACCTTTTGCTCTATACAGCATAGCAAGCAC

                                      *                      
      13982 C-AGAAAGCACATATCATGACAATTTTCTATCCCAATTCGGCCAATGTC
         66 CGA-AAAGCACATATCATGACAATTTCCTATCCCAATTCGGCCAATGTC

              
      14030 TG
          1 TG

      14032 CATTTAAAAA


Statistics
Matches: 111,  Mismatches: 3, Indels: 2
        0.96            0.03        0.02

Matches are distributed among these distances:
 112    1  0.01
 113  110  0.99

ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27


Consensus pattern (113 bp):   
TGATATGAATATTTCCCAGCAGTAATACACAGAAAACCTTTTGCTCTATACAGCATAGCAAGCAC
CGAAAAGCACATATCATGACAATTTCCTATCCCAATTCGGCCAATGTC

Found at i:17178 original size:153 final size:153

Alignment explanation


    Indices: 16900--17333  Score: 744
    Period size: 153  Copynumber: 2.8  Consensus size: 153

      16890 TAGCACACAG

                                                                             
      16900 GTGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATA
          1 GTGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATA

             * *       *                                                     
      16965 AGAGTTCCATTACCAACCTTTATTCAGATGCACCATTATACCTTAATGTATAATAGGAATGCTAC
         66 AAAATTCCATTGCCAACCTTTATTCAGATGCACCATTATACCTTAATGTATAATAGGAATGCTAC

                                   
      17030 TGTTATTAAAGTATATTACTCAA
        131 TGTTATTAAAGTATATTACTCAA

                                                     *               *       
      17053 GTGGCACCACTATACCTTTATGTATAATAGGAATGCCACCATATTGTGCCTTTTACTACATAATA
          1 GTGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATA

                                             *                               
      17118 AAAATTCTCATTGCCAACCTTTATTCAGATGCATCATTATACCTTAATGTAT-ATAGGAATGCTA
         66 AAAATTC-CATTGCCAACCTTTATTCAGATGCACCATTATACCTTAATGTATAATAGGAATGCTA

                                    
      17182 CTGTTATTAAAGTATATTACTCAA
        130 CTGTTATTAAAGTATATTACTCAA

            *             *                               *                  
      17206 ATGGCACCACTATAACTTTATGTATAATAGGAATGCCACCACATTGAGCCTTTTACTGCATAATA
          1 GTGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATA

                     *                 *                                   
      17271 AAAATTCCCGTTGCCAACCTTTATTCATATGCACCATTATACCTTAATGTATAATAGGAATGC
         66 AAAATT-CCATTGCCAACCTTTATTCAGATGCACCATTATACCTTAATGTATAATAGGAATGC

      17334 AGACTAAAGG


Statistics
Matches: 264,  Mismatches: 14, Indels: 5
        0.93            0.05        0.02

Matches are distributed among these distances:
 153  211  0.80
 154   53  0.20

ACGTcount: A:0.33, C:0.20, G:0.12, T:0.34


Consensus pattern (153 bp):   
GTGGCACCACTATACCTTTATGTATAATAGGAATGCCACCACATTGTGCCTTTTACTGCATAATA
AAAATTCCATTGCCAACCTTTATTCAGATGCACCATTATACCTTAATGTATAATAGGAATGCTAC
TGTTATTAAAGTATATTACTCAA
Done.