Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005207.1 Corchorus capsularis cultivar CVL-1 contig05225, 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: 5381
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38


Found at i:574 original size:12 final size:12

Alignment explanation


    Indices: 557--586  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

        547 CGCAGTTTCG

                        
        557 TCGCAAAGTTCA
          1 TCGCAAAGTTCA

                        
        569 TCGCAAAGTTCA
          1 TCGCAAAGTTCA

             *    
        581 TTGCAA
          1 TCGCAA

        587 CAGGCAAAAG


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

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27


Consensus pattern (12 bp):   
TCGCAAAGTTCA

Found at i:4032 original size:19 final size:20

Alignment explanation


    Indices: 3996--4039  Score: 58
    Period size: 19  Copynumber: 2.4  Consensus size: 20

       3986 TTTAGTTTAG

                          *     
       3996 TCAG-TTTTTTGAGTTCAGT
          1 TCAGTTTTTTTGAGATCAGT

                                
       4015 TCAGTTTTTTTGA-ATCAGT
          1 TCAGTTTTTTTGAGATCAGT

                   
       4034 T-AGTTT
          1 TCAGTTT

       4040 GAGTCTGAGT


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  18    5  0.22
  19   10  0.43
  20    8  0.35

ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55


Consensus pattern (20 bp):   
TCAGTTTTTTTGAGATCAGT

Found at i:5334 original size:17 final size:17

Alignment explanation


    Indices: 5312--5370  Score: 68
    Period size: 17  Copynumber: 3.6  Consensus size: 17

       5302 AAACTATTGG

                       *     
       5312 AATTTTAACTTGTTAAT
          1 AATTTTAACTTATTAAT

                           **
       5329 AATTTTAAC-TATT-GG
          1 AATTTTAACTTATTAAT

                    *        
       5344 AATTTTAATTTATTAAT
          1 AATTTTAACTTATTAAT

                      
       5361 AATTTTAACT
          1 AATTTTAACT

       5371 ATTGCAATTT


Statistics
Matches: 33,  Mismatches: 7, Indels: 4
        0.75            0.16        0.09

Matches are distributed among these distances:
  15    8  0.24
  16    7  0.21
  17   18  0.55

ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53


Consensus pattern (17 bp):   
AATTTTAACTTATTAAT

Found at i:5344 original size:32 final size:32

Alignment explanation


    Indices: 5303--5381  Score: 131
    Period size: 32  Copynumber: 2.5  Consensus size: 32

       5293 TGCTCAAAAA

                                *           
       5303 AACTATTGGAATTTTAACTTGTTAATAATTTT
          1 AACTATTGGAATTTTAACTTATTAATAATTTT

                             *              
       5335 AACTATTGGAATTTTAATTTATTAATAATTTT
          1 AACTATTGGAATTTTAACTTATTAATAATTTT

                    *      
       5367 AACTATTGCAATTTT
          1 AACTATTGGAATTTT


Statistics
Matches: 44,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  32   44  1.00

ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51


Consensus pattern (32 bp):   
AACTATTGGAATTTTAACTTATTAATAATTTT
Done.