Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016689.1 Corchorus olitorius cultivar O-4 contig16722, 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: 23963
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:2102 original size:20 final size:21

Alignment explanation


    Indices: 2079--2123  Score: 58
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       2069 CTTTTTTGCA

                                  
       2079 CATGAG-TCTCACGCAAA-CTG
          1 CATGAGATCTCACG-AAACCTG

                                  
       2099 CATGAGTATCTCACGAAACCTG
          1 CATGAG-ATCTCACGAAACCTG

               
       2121 CAT
          1 CAT

       2124 ATGATTGCAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  20    6  0.27
  21    3  0.14
  22   13  0.59

ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22


Consensus pattern (21 bp):   
CATGAGATCTCACGAAACCTG

Found at i:7071 original size:7 final size:6

Alignment explanation


    Indices: 7047--7076  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       7037 CCAAATAGGG

                          *                   
       7047 AGAAAA AGAAAA GGAAAA AGAAAA AGAAAA
          1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA

       7077 TATAACCTCC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00


Consensus pattern (6 bp):   
AGAAAA

Found at i:13771 original size:6 final size:6

Alignment explanation


    Indices: 13755--13793  Score: 55
    Period size: 6  Copynumber: 6.8  Consensus size: 6

      13745 TGTATAGGTT

                                                  *        
      13755 GGTTC- GGTTCG GGTTCG GGTTCG GGTTC- GGTACG GGTTC
          1 GGTTCG GGTTCG GGTTCG GGTTCG GGTTCG GGTTCG GGTTC

      13794 CATGAAATGA


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
   5    9  0.30
   6   21  0.70

ACGTcount: A:0.03, C:0.18, G:0.46, T:0.33


Consensus pattern (6 bp):   
GGTTCG

Found at i:13771 original size:11 final size:11

Alignment explanation


    Indices: 13755--13793  Score: 60
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      13745 TGTATAGGTT

                       
      13755 GGTTCGGTTCG
          1 GGTTCGGTTCG

                        
      13766 GGTTCGGGTTCG
          1 GGTTC-GGTTCG

                    *  
      13778 GGTTCGGTACG
          1 GGTTCGGTTCG

                 
      13789 GGTTC
          1 GGTTC

      13794 CATGAAATGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  11   15  0.58
  12   11  0.42

ACGTcount: A:0.03, C:0.18, G:0.46, T:0.33


Consensus pattern (11 bp):   
GGTTCGGTTCG

Found at i:13777 original size:17 final size:17

Alignment explanation


    Indices: 13755--13793  Score: 53
    Period size: 17  Copynumber: 2.3  Consensus size: 17

      13745 TGTATAGGTT

                          *  
      13755 GGTTCGGTTCGGGTTCG
          1 GGTTCGGTTCGGGTACG

                              
      13772 GGTTCGGGTTC-GGTACG
          1 GGTTC-GGTTCGGGTACG

                 
      13789 GGTTC
          1 GGTTC

      13794 CATGAAATGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  17   15  0.75
  18    5  0.25

ACGTcount: A:0.03, C:0.18, G:0.46, T:0.33


Consensus pattern (17 bp):   
GGTTCGGTTCGGGTACG

Found at i:22496 original size:49 final size:47

Alignment explanation


    Indices: 22390--22531  Score: 140
    Period size: 49  Copynumber: 2.9  Consensus size: 47

      22380 CAAGCACTCT

                *                            **            *
      22390 TTTACTTTTCCTGCACTTTTTTCTCAATTTTTACTACAAAATTGAACC
          1 TTTAATTTTCCTGCAC-TTTTTCTCAATTTTTAAGACAAAATTGAACA

                *               *                          * 
      22438 TTTATTTTTCCTCGCACATTATTCTCAATTTTTAAGACAAAATTGAATA
          1 TTTAATTTTCCT-GCAC-TTTTTCTCAATTTTTAAGACAAAATTGAACA

                       *   *      *         **           
      22487 TTTAATTTTCATTGCTCTTTTTATCAATTTTTTGGACAAAATTGA
          1 TTTAATTTTC-CTGCACTTTTTCTCAATTTTTAAGACAAAATTGA

      22532 TTGGCACGCT


Statistics
Matches: 78,  Mismatches: 14, Indels: 4
        0.81            0.15        0.04

Matches are distributed among these distances:
  48   35  0.45
  49   42  0.54
  50    1  0.01

ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49


Consensus pattern (47 bp):   
TTTAATTTTCCTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACA
Done.