Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016780.1 Corchorus olitorius cultivar O-4 contig16813, 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: 8581
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36


Found at i:5953 original size:38 final size:38

Alignment explanation


    Indices: 5854--5994  Score: 185
    Period size: 38  Copynumber: 3.7  Consensus size: 38

       5844 GGCTGTGCAT

                                                    
       5854 AGTGGACCCGTACCTCAGGGGGTTAAACTGA-TGGTAAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACT-ATTGGT-AAG

                   * *    *                       
       5893 AGTGGACACATACCACAGGGGGTTAAACTATTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTATTGGTAAG

                       *   * *           *        
       5931 AGTGGACCCGTGCCTTACGGGGTTAAACTGTTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTATTGGTAAG

                       *              
       5969 AGTGGACCCGTGCCTCAGGGGGTTAA
          1 AGTGGACCCGTACCTCAGGGGGTTAA

       5995 CTGTTGACTA


Statistics
Matches: 89,  Mismatches: 12, Indels: 3
        0.86            0.12        0.03

Matches are distributed among these distances:
  38   59  0.66
  39   30  0.34

ACGTcount: A:0.26, C:0.18, G:0.33, T:0.22


Consensus pattern (38 bp):   
AGTGGACCCGTACCTCAGGGGGTTAAACTATTGGTAAG

Found at i:6044 original size:6 final size:6

Alignment explanation


    Indices: 6033--6068  Score: 72
    Period size: 6  Copynumber: 6.0  Consensus size: 6

       6023 TTAACGGATA

                                                     
       6033 ATTGTG ATTGTG ATTGTG ATTGTG ATTGTG ATTGTG
          1 ATTGTG ATTGTG ATTGTG ATTGTG ATTGTG ATTGTG

       6069 GTGCAGCTTG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   30  1.00

ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50


Consensus pattern (6 bp):   
ATTGTG

Found at i:8366 original size:70 final size:69

Alignment explanation


    Indices: 8238--8398  Score: 277
    Period size: 70  Copynumber: 2.3  Consensus size: 69

       8228 CAGATCTTGG

                                 *                                           
       8238 CCAAGTCCTGTCCAGGACTTGGGCTGTTAGGAACGCAGAAATACAGGACAAGACCTGGGCAGGAG
          1 CCAAGTCCTGTCCAGGACTTGTGCTGTTAGGAACGCAGAAATACAGGACAAGACCTGGGCAGGAG

                
       8303 TTAC
         66 TTAC

                         *                   *                               
       8307 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGCAGAAATACAGGACAAGACCTGGGCAGGA
          1 CCAAGTCCTGTCCAGGACTTGTGCTGTT-AGGAACGCAGAAATACAGGACAAGACCTGGGCAGGA

                 
       8372 GTTAC
         65 GTTAC

                             *    
       8377 CCAAGTCCTGTCCAGGAGTTGT
          1 CCAAGTCCTGTCCAGGACTTGT

       8399 TGCGGGAAAT


Statistics
Matches: 86,  Mismatches: 5, Indels: 1
        0.93            0.05        0.01

Matches are distributed among these distances:
  69   26  0.30
  70   60  0.70

ACGTcount: A:0.26, C:0.24, G:0.30, T:0.19


Consensus pattern (69 bp):   
CCAAGTCCTGTCCAGGACTTGTGCTGTTAGGAACGCAGAAATACAGGACAAGACCTGGGCAGGAG
TTAC
Done.