Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009645.1 Corchorus olitorius cultivar O-4 contig09677, 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: 5865
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:100 original size:21 final size:21

Alignment explanation


    Indices: 76--121  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

         66 ATGTCATTCT

                                 
         76 TGATATTAAGGAAGAATCAAG
          1 TGATATTAAGGAAGAATCAAG

                *  **      *     
         97 TGATGTTGTGGAAGAGTCAAG
          1 TGATATTAAGGAAGAATCAAG

                
        118 TGAT
          1 TGAT

        122 GTTGCTGAAA


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.37, C:0.04, G:0.30, T:0.28


Consensus pattern (21 bp):   
TGATATTAAGGAAGAATCAAG

Found at i:122 original size:21 final size:21

Alignment explanation


    Indices: 85--135  Score: 75
    Period size: 21  Copynumber: 2.4  Consensus size: 21

         75 TTGATATTAA

                                 
         85 GGAAGAATCAAGTGATGTTGT
          1 GGAAGAATCAAGTGATGTTGT

                  *               
        106 GGAAGAGTCAAGTGATGTTGCT
          1 GGAAGAATCAAGTGATGTTG-T

             *      
        128 GAAAGAAT
          1 GGAAGAAT

        136 GAATACCGGG


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  21   19  0.73
  22    7  0.27

ACGTcount: A:0.35, C:0.06, G:0.33, T:0.25


Consensus pattern (21 bp):   
GGAAGAATCAAGTGATGTTGT

Found at i:3436 original size:21 final size:21

Alignment explanation


    Indices: 3387--3436  Score: 82
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3377 ATGTCATTCT

                   *             
       3387 TGATGTTAAGGAAGAGTCAAG
          1 TGATGTTGAGGAAGAGTCAAG

                    *            
       3408 TGATGTTGTGGAAGAGTCAAG
          1 TGATGTTGAGGAAGAGTCAAG

                    
       3429 TGATGTTG
          1 TGATGTTG

       3437 CTGAAAGAAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30


Consensus pattern (21 bp):   
TGATGTTGAGGAAGAGTCAAG

Found at i:3449 original size:22 final size:21

Alignment explanation


    Indices: 3398--3449  Score: 77
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3388 GATGTTAAGG

                                *
       3398 AAGAGTCAAGTGATGTTGTGG
          1 AAGAGTCAAGTGATGTTGTGA

                                  
       3419 AAGAGTCAAGTGATGTTGCTGA
          1 AAGAGTCAAGTGATGTTG-TGA

                *    
       3441 AAGAATCAA
          1 AAGAGTCAA

       3450 TACCGGAGGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 1
        0.90            0.06        0.03

Matches are distributed among these distances:
  21   18  0.64
  22   10  0.36

ACGTcount: A:0.37, C:0.08, G:0.31, T:0.25


Consensus pattern (21 bp):   
AAGAGTCAAGTGATGTTGTGA
Done.