Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015150.1 Corchorus olitorius cultivar O-4 contig15183, 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: 18267
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:6626 original size:2 final size:2

Alignment explanation


    Indices: 6621--6665  Score: 67
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       6611 AAAAATTGGT

                                                 *                        
       6621 TA TA TA TA TA TA TA TA -A TA T- TA TT TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
       6661 TA TA T
          1 TA TA T

       6666 CTAAACTCAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
   1    2  0.05
   2   37  0.95

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:10013 original size:28 final size:28

Alignment explanation


    Indices: 9958--10013  Score: 69
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       9948 ATAAAGATGT

                        *    *  *       
       9958 AAATGAATAAGTTTTTTTTATTATAATA
          1 AAATGAATAAGTATTTTATAATATAATA

                                         
       9986 AAATGAATAAGTATTTTATACATA-AATA
          1 AAATGAATAAGTATTTTATA-ATATAATA

      10014 CATAATTATA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  28   22  0.92
  29    2  0.08

ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43


Consensus pattern (28 bp):   
AAATGAATAAGTATTTTATAATATAATA

Found at i:11671 original size:2 final size:2

Alignment explanation


    Indices: 11664--11690  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      11654 CCCAAACTTT

                                                    
      11664 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

      11691 TAATTTGTAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:12350 original size:18 final size:18

Alignment explanation


    Indices: 12324--12360  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      12314 TTCCCTTCAC

                *             
      12324 TTATTTATTCCTAAATAA
          1 TTATATATTCCTAAATAA

                     *        
      12342 TTATATATTTCTAAATAA
          1 TTATATATTCCTAAATAA

             
      12360 T
          1 T

      12361 ATTGAGGGGC


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

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51


Consensus pattern (18 bp):   
TTATATATTCCTAAATAA

Found at i:14839 original size:15 final size:15

Alignment explanation


    Indices: 14819--14847  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      14809 TATATATATA

                           
      14819 TAGTAGTGGTACTAC
          1 TAGTAGTGGTACTAC

                          
      14834 TAGTAGTGGTACTA
          1 TAGTAGTGGTACTA

      14848 GTACTAGTAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34


Consensus pattern (15 bp):   
TAGTAGTGGTACTAC

Found at i:14855 original size:15 final size:15

Alignment explanation


    Indices: 14822--14855  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      14812 ATATATATAG

                          *
      14822 TAGTGGTACTACTAG
          1 TAGTGGTACTACTAC

                       *   
      14837 TAGTGGTACTAGTAC
          1 TAGTGGTACTACTAC

                
      14852 TAGT
          1 TAGT

      14856 ACTTTGAATG


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

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35


Consensus pattern (15 bp):   
TAGTGGTACTACTAC

Found at i:15436 original size:29 final size:29

Alignment explanation


    Indices: 15403--15458  Score: 112
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      15393 CGACCTAAAC

                                         
      15403 TTACCATGTCTATAGAATGGTTTAATTTA
          1 TTACCATGTCTATAGAATGGTTTAATTTA

                                       
      15432 TTACCATGTCTATAGAATGGTTTAATT
          1 TTACCATGTCTATAGAATGGTTTAATT

      15459 ATACAATATG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   27  1.00

ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45


Consensus pattern (29 bp):   
TTACCATGTCTATAGAATGGTTTAATTTA

Found at i:15620 original size:2 final size:2

Alignment explanation


    Indices: 15613--15637  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      15603 GAGTCTCAAA

                                                 
      15613 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      15638 AACTATAGGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.