Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019988.1 Corchorus olitorius cultivar O-4 contig20021, 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: 13142
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:2953 original size:27 final size:26

Alignment explanation


    Indices: 2922--3010  Score: 97
    Period size: 27  Copynumber: 3.3  Consensus size: 26

       2912 ACCACACTGC

                     *               *
       2922 CCCCTGAAGCACAAATGACTAAAATA
          1 CCCCTGAAGTACAAATGACTAAAATG

                     *   *       *      
       2948 CTCCCTAGATGTAAAAATGACCAAAATG
          1 C-CCCT-GAAGTACAAATGACTAAAATG

                       *               
       2976 CCCCTGAACGTGCAAATGACTAAAATG
          1 CCCCTGAA-GTACAAATGACTAAAATG

                    
       3003 CCCCTGAA
          1 CCCCTGAA

       3011 TGTCCTTGAA


Statistics
Matches: 51,  Mismatches: 9, Indels: 5
        0.78            0.14        0.08

Matches are distributed among these distances:
  26    3  0.06
  27   31  0.61
  28   17  0.33

ACGTcount: A:0.40, C:0.27, G:0.15, T:0.18


Consensus pattern (26 bp):   
CCCCTGAAGTACAAATGACTAAAATG

Found at i:7676 original size:21 final size:21

Alignment explanation


    Indices: 7645--7705  Score: 113
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       7635 GCTCGGCAAT

                                  
       7645 CACCGAGCCATGCCGAGGCAGG
          1 CACC-AGCCATGCCGAGGCAGG

                                 
       7667 CACCAGCCATGCCGAGGCAGG
          1 CACCAGCCATGCCGAGGCAGG

                              
       7688 CACCAGCCATGCCGAGGC
          1 CACCAGCCATGCCGAGGC

       7706 CATGGCCCGG


Statistics
Matches: 39,  Mismatches: 0, Indels: 1
        0.98            0.00        0.03

Matches are distributed among these distances:
  21   35  0.90
  22    4  0.10

ACGTcount: A:0.23, C:0.39, G:0.33, T:0.05


Consensus pattern (21 bp):   
CACCAGCCATGCCGAGGCAGG

Found at i:8707 original size:11 final size:11

Alignment explanation


    Indices: 8691--8715  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       8681 AGAAAATTGT

                       
       8691 TTGTTTTTGGA
          1 TTGTTTTTGGA

                       
       8702 TTGTTTTTGGA
          1 TTGTTTTTGGA

               
       8713 TTG
          1 TTG

       8716 ATTATCCCCC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64


Consensus pattern (11 bp):   
TTGTTTTTGGA

Found at i:9677 original size:15 final size:16

Alignment explanation


    Indices: 9648--9677  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       9638 ATGTGAATTC

                            
       9648 AAATTGATCTTTTGAA
          1 AAATTGATCTTTTGAA

                           
       9664 AAATTGAT-TTTTGA
          1 AAATTGATCTTTTGA

       9678 TAAACTTACA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47


Consensus pattern (16 bp):   
AAATTGATCTTTTGAA

Found at i:12285 original size:21 final size:21

Alignment explanation


    Indices: 12242--12285  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      12232 CCAATTTAGA

                           *     
      12242 TTTAGATTTAAATTTCTTGTT
          1 TTTAGATTTAAATTTATTGTT

                                  
      12263 TTTAGATTTAAGATTTATT-TT
          1 TTTAGATTTAA-ATTTATTGTT

              
      12284 TT
          1 TT

      12286 ATGCATCTTA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21   15  0.71
  22    6  0.29

ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64


Consensus pattern (21 bp):   
TTTAGATTTAAATTTATTGTT
Done.