Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022210.1 Corchorus olitorius cultivar O-4 contig22243, 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: 6576
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:908 original size:12 final size:12

Alignment explanation


    Indices: 891--915  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        881 TCTTCATCAT

                        
        891 CGCTGTCACCTC
          1 CGCTGTCACCTC

                        
        903 CGCTGTCACCTC
          1 CGCTGTCACCTC

             
        915 C
          1 C

        916 AAACATGGCC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.08, C:0.52, G:0.16, T:0.24


Consensus pattern (12 bp):   
CGCTGTCACCTC

Found at i:5182 original size:80 final size:79

Alignment explanation


    Indices: 5079--5237  Score: 255
    Period size: 80  Copynumber: 2.0  Consensus size: 79

       5069 GCATTCGTTA

                                                                             
       5079 TGCAACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAG
          1 TGCAACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAG

                          
       5144 TCGTCTAAGATCCG
         66 TCGTCTAAGATCCG

                         *     *                             **  **          
       5158 TGCAACTCCCCCTTGTTTTTATTTCCCTTCCCAAAATAGGTTTTCCAGCTGACTTATCTTCAAAA
          1 TGCAACT-CCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA

                           
       5223 GTCGTCTAAGATCCG
         65 GTCGTCTAAGATCCG

       5238 AAACCACTTT


Statistics
Matches: 73,  Mismatches: 6, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  79    7  0.10
  80   66  0.90

ACGTcount: A:0.23, C:0.31, G:0.12, T:0.33


Consensus pattern (79 bp):   
TGCAACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAG
TCGTCTAAGATCCG

Found at i:6273 original size:20 final size:20

Alignment explanation


    Indices: 6245--6288  Score: 72
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       6235 AGAAGCATAA

                *               
       6245 ATATATATATCTATAACAAT
          1 ATATCTATATCTATAACAAT

                                
       6265 ATATCTATATCTATAACAAT
          1 ATATCTATATCTATAACAAT

                 
       6285 -TATC
          1 ATATC

       6289 GGGGGATTGG


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  19    4  0.17
  20   19  0.83

ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41


Consensus pattern (20 bp):   
ATATCTATATCTATAACAAT
Done.