Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008245.1 Corchorus capsularis cultivar CVL-1 contig08266, 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: 19026
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33


Found at i:784 original size:4 final size:4

Alignment explanation


    Indices: 775--837  Score: 117
    Period size: 4  Copynumber: 15.8  Consensus size: 4

        765 AGCTCTTATA

                             *                                         
        775 TATG TATG TATG TACG TATG TATG TATG TATG TATG TATG TATG TATG
          1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG

                              
        823 TATG TATG TATG TAT
          1 TATG TATG TATG TAT

        838 TATTGGCTCC


Statistics
Matches: 57,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   4   57  1.00

ACGTcount: A:0.25, C:0.02, G:0.24, T:0.49


Consensus pattern (4 bp):   
TATG

Found at i:4866 original size:2 final size:2

Alignment explanation


    Indices: 4859--4892  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       4849 TTGGACTTCG

                                                                
       4859 AT AT AT AT AT -T 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

       4893 GGCTCTGACG


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

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


Consensus pattern (2 bp):   
AT

Found at i:6039 original size:73 final size:72

Alignment explanation


    Indices: 5908--6042  Score: 216
    Period size: 72  Copynumber: 1.9  Consensus size: 72

       5898 TGATAATTTC

                                                                 *           
       5908 TTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTACTTTTCTTGAAAA
          1 TTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTACCTTTCTTGAAAA

                   
       5973 AGCAAAA
         66 AGCAAAA

                                  *           *               * *          
       5980 TTTTTTCTAAAGGTTGCTCTCAGACACTAAATTTTTTATAGATGTGTATCTTTCCTTTCTTGA
          1 TTTTTTCTAAAGGTTGCTCTCAAACACTAAA-TTCTTATAGATGTGTATCCTACCTTTCTTGA

       6043 CAATGCAATT


Statistics
Matches: 57,  Mismatches: 5, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  72   30  0.53
  73   27  0.47

ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44


Consensus pattern (72 bp):   
TTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTACCTTTCTTGAAAA
AGCAAAA

Found at i:6868 original size:2 final size:2

Alignment explanation


    Indices: 6861--6893  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       6851 ACATACATAC

                                                             
       6861 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 A

       6894 CATTTCAGAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:8046 original size:3 final size:3

Alignment explanation


    Indices: 8038--8077  Score: 80
    Period size: 3  Copynumber: 13.3  Consensus size: 3

       8028 TAGCAAAATC

                                                                 
       8038 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A

       8078 ACCATCACTC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   37  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
ATT

Done.