Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021742.1 Corchorus olitorius cultivar O-4 contig21775, 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: 10623
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:792 original size:19 final size:20

Alignment explanation


    Indices: 747--793  Score: 69
    Period size: 20  Copynumber: 2.4  Consensus size: 20

        737 TGTTGGGTTC

                       *        
        747 TTTTGCATATTTATATCACA
          1 TTTTGCATATTAATATCACA

                          *     
        767 TTTTGCATATTAATTTCACA
          1 TTTTGCATATTAATATCACA

                    
        787 -TTTGCAT
          1 TTTTGCAT

        794 CTGCATGATC


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  19    7  0.28
  20   18  0.72

ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51


Consensus pattern (20 bp):   
TTTTGCATATTAATATCACA

Found at i:5687 original size:166 final size:166

Alignment explanation


    Indices: 5413--5749  Score: 647
    Period size: 166  Copynumber: 2.0  Consensus size: 166

       5403 CCGTTGAAGT

                                                                             
       5413 TCCTGCACGAATTCAGCAAAATTTCAGGATCCTATTTTAACTTGGATTCTACTCTAGGATGACTT
          1 TCCTGCACGAATTCAGCAAAATTTCAGGATCCTATTTTAACTTGGATTCTACTCTAGGATGACTT

                                 *                                           
       5478 TTAATCTAACTTGGAGTCCAAGTTAGACCCTAAACCGTCCTAGACCTCTTTCCAAGTTAGGATTG
         66 TTAATCTAACTTGGAGTCCAAATTAGACCCTAAACCGTCCTAGACCTCTTTCCAAGTTAGGATTG

                                                
       5543 GAATTCCTAGGGTTATTTCCACTATAAATAGCCACC
        131 GAATTCCTAGGGTTATTTCCACTATAAATAGCCACC

                                                                    *        
       5579 TCCTGCACGAATTCAGCAAAATTTCAGGATCCTATTTTAACTTGGATTCTACTCTATGATGACTT
          1 TCCTGCACGAATTCAGCAAAATTTCAGGATCCTATTTTAACTTGGATTCTACTCTAGGATGACTT

                                                                        *    
       5644 TTAATCTAACTTGGAGTCCAAATTAGACCCTAAACCGTCCTAGACCTCTTTCCAAGTTAGTATTG
         66 TTAATCTAACTTGGAGTCCAAATTAGACCCTAAACCGTCCTAGACCTCTTTCCAAGTTAGGATTG

                                                
       5709 GAATTCCTAGGGTTATTTCCACTATAAATAGCCACC
        131 GAATTCCTAGGGTTATTTCCACTATAAATAGCCACC

                 
       5745 TCCTG
          1 TCCTG

       5750 TAACACAAAT


Statistics
Matches: 168,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 166  168  1.00

ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33


Consensus pattern (166 bp):   
TCCTGCACGAATTCAGCAAAATTTCAGGATCCTATTTTAACTTGGATTCTACTCTAGGATGACTT
TTAATCTAACTTGGAGTCCAAATTAGACCCTAAACCGTCCTAGACCTCTTTCCAAGTTAGGATTG
GAATTCCTAGGGTTATTTCCACTATAAATAGCCACC

Found at i:6537 original size:15 final size:16

Alignment explanation


    Indices: 6504--6542  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       6494 TTACTTTGTT

                            
       6504 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
       6520 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

                    
       6535 TTGCTTTT
          1 TTG-TTTT

       6543 TTTCAACCTC


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

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

ACGTcount: A:0.15, C:0.08, G:0.13, T:0.64


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:7104 original size:42 final size:42

Alignment explanation


    Indices: 7057--7160  Score: 190
    Period size: 42  Copynumber: 2.5  Consensus size: 42

       7047 TCATAAAAAA

                       * *                            
       7057 AATTTTCTTTTTAATTTTTGTTTAAGAAATTTTACTACTAAC
          1 AATTTTCTTTTGAGTTTTTGTTTAAGAAATTTTACTACTAAC

                                                      
       7099 AATTTTCTTTTGAGTTTTTGTTTAAGAAATTTTACTACTAAC
          1 AATTTTCTTTTGAGTTTTTGTTTAAGAAATTTTACTACTAAC

                                
       7141 AATTTTCTTTTGAGTTTTTG
          1 AATTTTCTTTTGAGTTTTTG

       7161 AGTTTTTCCA


Statistics
Matches: 60,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   60  1.00

ACGTcount: A:0.27, C:0.09, G:0.09, T:0.56


Consensus pattern (42 bp):   
AATTTTCTTTTGAGTTTTTGTTTAAGAAATTTTACTACTAAC

Found at i:10259 original size:21 final size:21

Alignment explanation


    Indices: 10233--10287  Score: 65
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      10223 CGGCCGTTCA

                       *   **    
      10233 CCGTGCCACCATCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
      10254 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
      10275 CCGTGCCATCACC
          1 CCGTGCCACCACC

      10288 ATTCAAAGCC


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   29  1.00

ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC
Done.