Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013060.1 Corchorus olitorius cultivar O-4 contig13093, 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: 20267
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32


Found at i:118 original size:40 final size:40

Alignment explanation


    Indices: 1--341  Score: 549
    Period size: 40  Copynumber: 8.5  Consensus size: 40

                                                     
          1 CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTTGCCCTTC
          1 CCCACCGGAAGGTGTTGTTTAAATACCCAG-TTTGCCCTTC

                                                     
         42 CCCACCGGAAGGTGTTGTTTAAAATACCCAGTTTGCCCTTC
          1 CCCACCGGAAGGTGTTGTTT-AAATACCCAGTTTGCCCTTC

                                                    
         83 CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTC
          1 CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTC

                    *                               
        123 CCCACCGGTAGGTGTTGTTTAAATACCCAGTTTGCCCTTC
          1 CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTC

                       *                            
        163 CCCACCGGAAGTTGTTGTTTAAATACCCAGTTTGCCCTTC
          1 CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTC

                                    *               
        203 CCCACCGGAAGGTGTTGTTTAAATGCCCAGTTTGCCCTTC
          1 CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTC

                        *                    *       
        243 CCCACCGGAAGGCGTTGTTTAAA-ACCCAAGTTCGCCCTTC
          1 CCCACCGGAAGGTGTTGTTTAAATACCC-AGTTTGCCCTTC

                 *            *     *   *       *   
        283 CCCACAGGAAGGTGTTGTCTAAATTCCCGGTTTGCCTTTC
          1 CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTC

                      *        
        323 CCCACCGGAAAGTGTTGTT
          1 CCCACCGGAAGGTGTTGTT

        342 CCCAGTTTGC


Statistics
Matches: 279,  Mismatches: 18, Indels: 7
        0.92            0.06        0.02

Matches are distributed among these distances:
  39    3  0.01
  40  213  0.76
  41   53  0.19
  42   10  0.04

ACGTcount: A:0.20, C:0.30, G:0.21, T:0.30


Consensus pattern (40 bp):   
CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTC

Found at i:4466 original size:21 final size:21

Alignment explanation


    Indices: 4440--4481  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4430 GCACCTTAGA

                        **       
       4440 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAAATTGAAAC

                                 
       4461 CAACTCCGATGAAATTGAAAC
          1 CAACTCCGATGAAATTGAAAC

       4482 TTCTTTGTGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19


Consensus pattern (21 bp):   
CAACTCCGATGAAATTGAAAC

Found at i:8512 original size:11 final size:11

Alignment explanation


    Indices: 8492--8521  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       8482 CTAAGGGTAA

                       
       8492 AGGAAAGAGCT
          1 AGGAAAGAGCT

                 *     
       8503 AGGAAGGAGCT
          1 AGGAAAGAGCT

                    
       8514 AGGAAAGA
          1 AGGAAAGA

       8522 TCCTACTCCT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  11   17  1.00

ACGTcount: A:0.47, C:0.07, G:0.40, T:0.07


Consensus pattern (11 bp):   
AGGAAAGAGCT

Found at i:8925 original size:21 final size:21

Alignment explanation


    Indices: 8899--8940  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8889 GCACCTTAGG

                                 
       8899 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

                                 
       8920 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

       8941 TTCTTTGTGT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19


Consensus pattern (21 bp):   
CAACTCCGATGAGCTTGAAAC

Found at i:12356 original size:35 final size:35

Alignment explanation


    Indices: 12315--12431  Score: 157
    Period size: 35  Copynumber: 3.3  Consensus size: 35

      12305 CCATATCATA

                        *     *                 
      12315 AAACCATTGTTCTGAGAACA-AAACTTAAGGATTAC
          1 AAACCATTGTTCCGAGAATAGAAA-TTAAGGATTAC

             *                             *   
      12350 ACACCATTGTTCCGAGAATAGAAATTAAGGAATAC
          1 AAACCATTGTTCCGAGAATAGAAATTAAGGATTAC

                                   *            
      12385 AAACCATTGTTCCGCA-AATAGAGATTAAGGATTAC
          1 AAACCATTGTTCCG-AGAATAGAAATTAAGGATTAC

                        
      12420 AAACCATTGTTC
          1 AAACCATTGTTC

      12432 TGCAAATAAA


Statistics
Matches: 73,  Mismatches: 7, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  35   69  0.95
  36    4  0.05

ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26


Consensus pattern (35 bp):   
AAACCATTGTTCCGAGAATAGAAATTAAGGATTAC

Found at i:16143 original size:19 final size:18

Alignment explanation


    Indices: 16119--16154  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      16109 TGAAGACTTA

                               
      16119 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      16138 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      16155 ATTATTTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT
Done.