Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020364.1 Corchorus olitorius cultivar O-4 contig20397, 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: 3899
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34


Found at i:93 original size:35 final size:35

Alignment explanation


    Indices: 47--117  Score: 133
    Period size: 35  Copynumber: 2.0  Consensus size: 35

         37 ATAAACGAAT

                                   *           
         47 ACTTAAATGAACAATAAACGAGCTTGTTCGTGAAC
          1 ACTTAAATGAACAATAAACGAGCATGTTCGTGAAC

                                               
         82 ACTTAAATGAACAATAAACGAGCATGTTCGTGAAC
          1 ACTTAAATGAACAATAAACGAGCATGTTCGTGAAC

             
        117 A
          1 A

        118 TAAACGAACT


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  35   35  1.00

ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24


Consensus pattern (35 bp):   
ACTTAAATGAACAATAAACGAGCATGTTCGTGAAC

Found at i:338 original size:22 final size:21

Alignment explanation


    Indices: 287--389  Score: 68
    Period size: 22  Copynumber: 4.8  Consensus size: 21

        277 TATTAACGAC

                         *       
        287 ACTCTA-A-GAAAATTTGATA
          1 ACTCTATATGAAATTTTGATA

                * *            *  
        306 ACCTTTTTATGAAATTTTGGTA
          1 A-CTCTATATGAAATTTTGATA

                  *    *          
        328 ACGTCTGTATGGAATTTTGATA
          1 AC-TCTATATGAAATTTTGATA

                         **        
        350 ACTAC-ACTATGACGTTTTGATA
          1 ACT-CTA-TATGAAATTTTGATA

                              
        372 ACCTCTATATGAAATTTT
          1 A-CTCTATATGAAATTTT

        390 AGTAACCACA


Statistics
Matches: 62,  Mismatches: 14, Indels: 13
        0.70            0.16        0.15

Matches are distributed among these distances:
  19    1  0.02
  20    3  0.05
  21    3  0.05
  22   52  0.84
  23    3  0.05

ACGTcount: A:0.33, C:0.13, G:0.14, T:0.41


Consensus pattern (21 bp):   
ACTCTATATGAAATTTTGATA

Found at i:361 original size:44 final size:44

Alignment explanation


    Indices: 313--419  Score: 117
    Period size: 44  Copynumber: 2.4  Consensus size: 44

        303 ATAACCTTTT

                        *    *   *    *             *    
        313 TATGAAATTTTGGTAACGTCTGTATGGAATTTT-GATAACTACAC
          1 TATGAAATTTTGATAACCTCTATATGAAATTTTAG-TAACCACAC

                 **                                     
        357 TATGACGTTTTGATAACCTCTATATGAAATTTTAGTAACCACAC
          1 TATGAAATTTTGATAACCTCTATATGAAATTTTAGTAACCACAC

                   *     *     
        401 TATGAAAATTTGACAACCT
          1 TATGAAATTTTGATAACCT

        420 TCCTATGTAA


Statistics
Matches: 51,  Mismatches: 11, Indels: 2
        0.80            0.17        0.03

Matches are distributed among these distances:
  44   50  0.98
  45    1  0.02

ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Consensus pattern (44 bp):   
TATGAAATTTTGATAACCTCTATATGAAATTTTAGTAACCACAC

Found at i:767 original size:17 final size:17

Alignment explanation


    Indices: 745--780  Score: 63
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        735 TATAGGGTAA

                         *   
        745 TTGAAACTGAGTTTAGT
          1 TTGAAACTGAGTTAAGT

                             
        762 TTGAAACTGAGTTAAGT
          1 TTGAAACTGAGTTAAGT

              
        779 TT
          1 TT

        781 CCATTATCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42


Consensus pattern (17 bp):   
TTGAAACTGAGTTAAGT

Found at i:1904 original size:120 final size:118

Alignment explanation


    Indices: 1638--1984  Score: 585
    Period size: 120  Copynumber: 2.9  Consensus size: 118

       1628 TGTTAACGCA

                *                                                            
       1638 TTTGAGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
          1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA

                    *                                      *     
       1703 AAATTTAATGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCG
         66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTAGAGCG

                                                 *    *                      
       1756 TTTGGGA-CTTAAGAATTAAGGAGTAATTTATACTATGTTTAATGGAAGAGTTGGTTTGAAGTGG
          1 TTTGGGATC-TAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGG

                                                                    
       1820 AAAATTTAAGGACTTGAGAAATTCCTCAAAACAATATTCATGGTTGTGGTAGAGCG
         65 AAAATTTAAGGACTT--GAAATTCCTCAAAACAATATTCATGGTTGTGGTAGAGCG

                                                                        *    
       1876 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGA
          1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA

                                                           
       1941 AAA-TT--GGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGT
         66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGT

       1985 GGATGTTCTT


Statistics
Matches: 217,  Mismatches: 8, Indels: 11
        0.92            0.03        0.05

Matches are distributed among these distances:
 115   33  0.15
 117    7  0.03
 118   73  0.34
 119    2  0.01
 120  101  0.47
 121    1  0.00

ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36


Consensus pattern (118 bp):   
TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTAGAGCG
Done.