Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010342.1 Corchorus olitorius cultivar O-4 contig10374, 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: 9867
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:424 original size:16 final size:17

Alignment explanation


    Indices: 403--436  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        393 GTACGTATAA

                        *    
        403 ATTATAT-TCAATAAAT
          1 ATTATATATCAACAAAT

                             
        419 ATTATATATCAACAAAT
          1 ATTATATATCAACAAAT

             
        436 A
          1 A

        437 AAAAATAAAA


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

Matches are distributed among these distances:
  16    7  0.44
  17    9  0.56

ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38


Consensus pattern (17 bp):   
ATTATATATCAACAAAT

Found at i:760 original size:16 final size:16

Alignment explanation


    Indices: 739--769  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        729 ACCTGTTTAN

                            
        739 GGTTCGGGCCGGGCCG
          1 GGTTCGGGCCGGGCCG

                     *     
        755 GGTTCGGGCTGGGCC
          1 GGTTCGGGCCGGGCC

        770 TAGCCTTAAG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.00, C:0.29, G:0.55, T:0.16


Consensus pattern (16 bp):   
GGTTCGGGCCGGGCCG

Found at i:2907 original size:25 final size:25

Alignment explanation


    Indices: 2873--2947  Score: 141
    Period size: 25  Copynumber: 3.0  Consensus size: 25

       2863 TTCCATGCGG

                                     
       2873 CACGGGAGGTTGTGGCAAATGAGAC
          1 CACGGGAGGTTGTGGCAAATGAGAC

                *                    
       2898 CACGAGAGGTTGTGGCAAATGAGAC
          1 CACGGGAGGTTGTGGCAAATGAGAC

                                     
       2923 CACGGGAGGTTGTGGCAAATGAGAC
          1 CACGGGAGGTTGTGGCAAATGAGAC

       2948 AAAAGGAATA


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   48  1.00

ACGTcount: A:0.29, C:0.16, G:0.39, T:0.16


Consensus pattern (25 bp):   
CACGGGAGGTTGTGGCAAATGAGAC

Found at i:9052 original size:11 final size:11

Alignment explanation


    Indices: 9036--9060  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       9026 CGCGCTCAAA

                       
       9036 GCTGCGGATGG
          1 GCTGCGGATGG

                       
       9047 GCTGCGGATGG
          1 GCTGCGGATGG

               
       9058 GCT
          1 GCT

       9061 TGTGATGGGC


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

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.08, C:0.20, G:0.52, T:0.20


Consensus pattern (11 bp):   
GCTGCGGATGG
Done.