Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015167.1 Corchorus capsularis cultivar CVL-1 contig15188, 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: 50266
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:5537 original size:2 final size:2

Alignment explanation


    Indices: 5530--5566  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       5520 ATTGTAAGTC

                                                                   
       5530 TA TA TA TA TA 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 TA TA TA TA TA T

       5567 TTGCTCATCT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:13770 original size:18 final size:18

Alignment explanation


    Indices: 13747--13800  Score: 90
    Period size: 18  Copynumber: 3.0  Consensus size: 18

      13737 GAGTTAATGT

                  *           
      13747 CGATGGAGATTCAAAAAC
          1 CGATGGGGATTCAAAAAC

                              
      13765 CGATGGGGATTCAAAAAC
          1 CGATGGGGATTCAAAAAC

             *                
      13783 CAATGGGGATTCAAAAAC
          1 CGATGGGGATTCAAAAAC

      13801 ATACAAGGTG


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   34  1.00

ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17


Consensus pattern (18 bp):   
CGATGGGGATTCAAAAAC

Found at i:14863 original size:71 final size:71

Alignment explanation


    Indices: 14773--14923  Score: 275
    Period size: 71  Copynumber: 2.1  Consensus size: 71

      14763 TATGATTTTT

                *   *                                                       *
      14773 ATTTCGTTCCATTAATTAAACATTATTTGAGAGACCATTGTACTATTCTATTATTAAGTTCATGT
          1 ATTTTGTTACATTAATTAAACATTATTTGAGAGACCATTGTACTATTCTATTATTAAGTTCATGC

                  
      14838 CATCAA
         66 CATCAA

                                                                             
      14844 ATTTTGTTACATTAATTAAACATTATTTGAGAGACCATTGTACTATTCTATTATTAAGTTCATGC
          1 ATTTTGTTACATTAATTAAACATTATTTGAGAGACCATTGTACTATTCTATTATTAAGTTCATGC

                  
      14909 CATCAA
         66 CATCAA

                     
      14915 ATTTTGTTA
          1 ATTTTGTTA

      14924 AGACAAATTT


Statistics
Matches: 77,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  71   77  1.00

ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44


Consensus pattern (71 bp):   
ATTTTGTTACATTAATTAAACATTATTTGAGAGACCATTGTACTATTCTATTATTAAGTTCATGC
CATCAA

Found at i:14968 original size:32 final size:32

Alignment explanation


    Indices: 14927--14990  Score: 128
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      14917 TTTGTTAAGA

                                            
      14927 CAAATTTTGAATTCGAAGTCAGCATATTTGGT
          1 CAAATTTTGAATTCGAAGTCAGCATATTTGGT

                                            
      14959 CAAATTTTGAATTCGAAGTCAGCATATTTGGT
          1 CAAATTTTGAATTCGAAGTCAGCATATTTGGT

      14991 TTCCTATTGT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   32  1.00

ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38


Consensus pattern (32 bp):   
CAAATTTTGAATTCGAAGTCAGCATATTTGGT

Found at i:26373 original size:12 final size:12

Alignment explanation


    Indices: 26356--26380  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      26346 AAATTAGTCG

                        
      26356 ACCATTATAGCC
          1 ACCATTATAGCC

                        
      26368 ACCATTATAGCC
          1 ACCATTATAGCC

             
      26380 A
          1 A

      26381 TTTGATTAGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.36, C:0.32, G:0.08, T:0.24


Consensus pattern (12 bp):   
ACCATTATAGCC

Found at i:38817 original size:4 final size:4

Alignment explanation


    Indices: 38808--38836  Score: 58
    Period size: 4  Copynumber: 7.2  Consensus size: 4

      38798 TAAAGGTTCT

                                                
      38808 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
          1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T

      38837 CATGATTCAT


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

Matches are distributed among these distances:
   4   25  1.00

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (4 bp):   
TTTC

Found at i:45883 original size:2 final size:2

Alignment explanation


    Indices: 45876--45903  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      45866 TTTCTTGCAC

                                                     
      45876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      45904 GTGCTTTCCA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.