Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011463.1 Corchorus capsularis cultivar CVL-1 contig11484, 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: 7186
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:395 original size:22 final size:22

Alignment explanation


    Indices: 369--415  Score: 85
    Period size: 22  Copynumber: 2.1  Consensus size: 22

        359 ATTTATTCAT

                                  
        369 TATTAATTAACTATTAATTAGA
          1 TATTAATTAACTATTAATTAGA

                     *            
        391 TATTAATTAGCTATTAATTAGA
          1 TATTAATTAACTATTAATTAGA

               
        413 TAT
          1 TAT

        416 AGTATAATGG


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47


Consensus pattern (22 bp):   
TATTAATTAACTATTAATTAGA

Found at i:411 original size:11 final size:11

Alignment explanation


    Indices: 369--411  Score: 68
    Period size: 11  Copynumber: 3.9  Consensus size: 11

        359 ATTTATTCAT

                     * 
        369 TATTAATTAAC
          1 TATTAATTAGC

                      *
        380 TATTAATTAGA
          1 TATTAATTAGC

                       
        391 TATTAATTAGC
          1 TATTAATTAGC

                      
        402 TATTAATTAG
          1 TATTAATTAG

        412 ATATAGTATA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  11   29  1.00

ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47


Consensus pattern (11 bp):   
TATTAATTAGC

Found at i:3211 original size:32 final size:32

Alignment explanation


    Indices: 3169--3237  Score: 111
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       3159 GGTGCTAGAT

                                  *  *      
       3169 GCCGCAAAATAGCGGCGTCTTCTTTTTCAAAC
          1 GCCGCAAAATAGCGGCGTCTTCCTTCTCAAAC

                 *                          
       3201 GCCGCGAAATAGCGGCGTCTTCCTTCTCAAAC
          1 GCCGCAAAATAGCGGCGTCTTCCTTCTCAAAC

                 
       3233 GCCGC
          1 GCCGC

       3238 TATTTTAATA


Statistics
Matches: 34,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  32   34  1.00

ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23


Consensus pattern (32 bp):   
GCCGCAAAATAGCGGCGTCTTCCTTCTCAAAC

Found at i:3776 original size:10 final size:10

Alignment explanation


    Indices: 3761--3785  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       3751 GTTGTTTGAT

                      
       3761 TTTTGTGGAA
          1 TTTTGTGGAA

                      
       3771 TTTTGTGGAA
          1 TTTTGTGGAA

                 
       3781 TTTTG
          1 TTTTG

       3786 GTGTTTGTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56


Consensus pattern (10 bp):   
TTTTGTGGAA
Done.