Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004447.1 Corchorus capsularis cultivar CVL-1 contig04455, 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, 748

Length: 1247
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37


Found at i:204 original size:18 final size:18

Alignment explanation


    Indices: 181--216  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        171 AAGGTAAGCC

                              
        181 TATTTATTTCTGGTTCTA
          1 TATTTATTTCTGGTTCTA

                              
        199 TATTTATTTCTGGTTCTA
          1 TATTTATTTCTGGTTCTA

        217 AGAGTAGTAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61


Consensus pattern (18 bp):   
TATTTATTTCTGGTTCTA

Found at i:292 original size:45 final size:45

Alignment explanation


    Indices: 228--317  Score: 171
    Period size: 45  Copynumber: 2.0  Consensus size: 45

        218 GAGTAGTAGT

                 *                                       
        228 TCTAGTGGCCGACTCTCTTCTTTCAAATAGTTTCTCATTATTAAG
          1 TCTAGCGGCCGACTCTCTTCTTTCAAATAGTTTCTCATTATTAAG

                                                         
        273 TCTAGCGGCCGACTCTCTTCTTTCAAATAGTTTCTCATTATTAAG
          1 TCTAGCGGCCGACTCTCTTCTTTCAAATAGTTTCTCATTATTAAG

        318 AAAGGGTAAC


Statistics
Matches: 44,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   44  1.00

ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41


Consensus pattern (45 bp):   
TCTAGCGGCCGACTCTCTTCTTTCAAATAGTTTCTCATTATTAAG

Found at i:803 original size:10 final size:10

Alignment explanation


    Indices: 788--825  Score: 53
    Period size: 10  Copynumber: 4.0  Consensus size: 10

        778 ATAGAGTATT

                      
        788 ATTAATATAA
          1 ATTAATATAA

                      
        798 ATTAATAT--
          1 ATTAATATAA

               *      
        806 ATTTATATAA
          1 ATTAATATAA

                      
        816 ATTAATATAA
          1 ATTAATATAA

        826 TAAATAAATA


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
   8    7  0.29
  10   17  0.71

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (10 bp):   
ATTAATATAA

Found at i:813 original size:18 final size:18

Alignment explanation


    Indices: 787--834  Score: 71
    Period size: 18  Copynumber: 2.7  Consensus size: 18

        777 AATAGAGTAT

                              
        787 TATTAATATAAATTAATA
          1 TATTAATATAAATTAATA

                *             
        805 TATTTATATAAATTAATA
          1 TATTAATATAAATTAATA

              *          
        823 TAATAA-ATAAAT
          1 TATTAATATAAAT

        835 ATGCATTAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  17    6  0.22
  18   21  0.78

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (18 bp):   
TATTAATATAAATTAATA

Found at i:867 original size:18 final size:16

Alignment explanation


    Indices: 826--858  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        816 ATTAATATAA

                            
        826 TAAAT-AAATATGCAT
          1 TAAATAAAATATGCAT

                            
        841 TAAATAAAATATGCAT
          1 TAAATAAAATATGCAT

              
        857 TA
          1 TA

        859 TATATAAAAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    5  0.29
  16   12  0.71

ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33


Consensus pattern (16 bp):   
TAAATAAAATATGCAT
Done.