Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015132.1 Corchorus olitorius cultivar O-4 contig15165, 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: 11807
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34


Found at i:2205 original size:49 final size:47

Alignment explanation


    Indices: 2086--2229  Score: 139
    Period size: 49  Copynumber: 3.0  Consensus size: 47

       2076 CCAAGCAATC

                 *                             **          *
       2086 CTTTACTTTTCA-CTGCACTTTTTATCAATTTTTACTACAAAATTGAA
          1 CTTTAATTTTCATC-GCACTTTTTATCAATTTTTAAGACAAAATTGAT

                *     *   **         *                        
       2133 CTTTTATTTTTACTTACATCTTTTTCTCAATTTTTAAAGACAAAATTGAT
          1 CTTTAATTTTCA-TCGCA-CTTTTTATCAATTTTT-AAGACAAAATTGAT

                                               *            
       2183 CTCTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGAT
          1 CT-TTAATTTTCATCGCACTTTTTATCAATTTTTAAGACAAAATTGAT

       2230 TGGCACGCTC


Statistics
Matches: 77,  Mismatches: 15, Indels: 10
        0.75            0.15        0.10

Matches are distributed among these distances:
  47   21  0.27
  48    2  0.03
  49   30  0.39
  50   16  0.21
  51    8  0.10

ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49


Consensus pattern (47 bp):   
CTTTAATTTTCATCGCACTTTTTATCAATTTTTAAGACAAAATTGAT

Found at i:4433 original size:28 final size:28

Alignment explanation


    Indices: 4401--4456  Score: 112
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       4391 AAAAACAATT

                                        
       4401 TTAGAAGAGGATGATCAAAACTGAAACA
          1 TTAGAAGAGGATGATCAAAACTGAAACA

                                        
       4429 TTAGAAGAGGATGATCAAAACTGAAACA
          1 TTAGAAGAGGATGATCAAAACTGAAACA

       4457 AGAGTAATTC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18


Consensus pattern (28 bp):   
TTAGAAGAGGATGATCAAAACTGAAACA

Found at i:9959 original size:14 final size:14

Alignment explanation


    Indices: 9940--9969  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       9930 CAACTTGAGC

                          
       9940 CAAATTTCAAGAGT
          1 CAAATTTCAAGAGT

                          
       9954 CAAATTTCAAGAGT
          1 CAAATTTCAAGAGT

              
       9968 CA
          1 CA

       9970 TCATACAAGC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27


Consensus pattern (14 bp):   
CAAATTTCAAGAGT

Found at i:11226 original size:2 final size:2

Alignment explanation


    Indices: 11219--11253  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      11209 ATTTTATTAG

                                                                
      11219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      11254 CTAGTTAAAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.