Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023398.1 Corchorus olitorius cultivar O-4 contig23431, 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: 13539
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:3945 original size:19 final size:20

Alignment explanation


    Indices: 3894--3945  Score: 56
    Period size: 19  Copynumber: 2.8  Consensus size: 20

       3884 ATGTAGGATT

                                
       3894 TTTAATAA-TAATTATTCAA
          1 TTTAATAATTAATTATTCAA

             **               * 
       3913 TAAAATAATT-ATTATT-TA
          1 TTTAATAATTAATTATTCAA

                           
       3931 TTTAATAATTAATTA
          1 TTTAATAATTAATTA

       3946 ATTTCAGCCC


Statistics
Matches: 26,  Mismatches: 5, Indels: 4
        0.74            0.14        0.11

Matches are distributed among these distances:
  18    9  0.35
  19   16  0.62
  20    1  0.04

ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50


Consensus pattern (20 bp):   
TTTAATAATTAATTATTCAA

Found at i:4315 original size:13 final size:13

Alignment explanation


    Indices: 4297--4322  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4287 AAGGTAGCAA

                         
       4297 CAAAAATCATCAC
          1 CAAAAATCATCAC

                         
       4310 CAAAAATCATCAC
          1 CAAAAATCATCAC

       4323 TCATGCCAAG


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

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15


Consensus pattern (13 bp):   
CAAAAATCATCAC

Found at i:8816 original size:15 final size:16

Alignment explanation


    Indices: 8784--8822  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       8774 TACTTTGTTC

                            
       8784 TGTTTTCTAGTATAAT
          1 TGTTTTCTAGTATAAT

                       *    
       8800 TGTTTTCT-GTTTAAT
          1 TGTTTTCTAGTATAAT

              *     
       8815 TGCTTTCT
          1 TGTTTTCT

       8823 TTCAACCTCT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.62
  16    8  0.38

ACGTcount: A:0.15, C:0.10, G:0.13, T:0.62


Consensus pattern (16 bp):   
TGTTTTCTAGTATAAT

Found at i:11798 original size:21 final size:21

Alignment explanation


    Indices: 11733--11804  Score: 63
    Period size: 21  Copynumber: 3.4  Consensus size: 21

      11723 CCACTACCAA

                 *         *      
      11733 GCCACAACCGGCCATTCACCGT
          1 GCCACCACCGGCCATGC-CCGT

                    *  ** *      
      11755 GCCACCACTGGTTAAGCCCGT
          1 GCCACCACCGGCCATGCCCGT

                              *  
      11776 GCCACCACCGGCCATGCCTGT
          1 GCCACCACCGGCCATGCCCGT

               *    
      11797 GCCGCCAC
          1 GCCACCAC

      11805 ATCAACTGTG


Statistics
Matches: 38,  Mismatches: 12, Indels: 1
        0.75            0.24        0.02

Matches are distributed among these distances:
  21   27  0.71
  22   11  0.29

ACGTcount: A:0.18, C:0.46, G:0.22, T:0.14


Consensus pattern (21 bp):   
GCCACCACCGGCCATGCCCGT
Done.