Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007333.1 Corchorus olitorius cultivar O-4 contig07358, 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, 784

Length: 1308
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44


Found at i:670 original size:31 final size:31

Alignment explanation


    Indices: 632--693  Score: 106
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        622 GAGTTTTGTA

                               *           
        632 AAACTTTTGAATCACCTATTATACCCTTATT
          1 AAACTTTTGAATCACCTATCATACCCTTATT

                                *          
        663 AAACTTTTGAATCACCTATCGTACCCTTATT
          1 AAACTTTTGAATCACCTATCATACCCTTATT

        694 TTTCGAATAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   29  1.00

ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40


Consensus pattern (31 bp):   
AAACTTTTGAATCACCTATCATACCCTTATT

Found at i:809 original size:14 final size:14

Alignment explanation


    Indices: 790--836  Score: 51
    Period size: 14  Copynumber: 3.2  Consensus size: 14

        780 TATCCTTATA

                          
        790 ACTATTTTATTTTT
          1 ACTATTTTATTTTT

                            
        804 ACTATTTTACTATTTT
          1 ACTATTTTA-T-TTTT

                      *    
        820 ACT-TTTATAGTTTT
          1 ACTATTT-TATTTTT

               
        834 ACT
          1 ACT

        837 CAACTAAAAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 6
        0.81            0.03        0.17

Matches are distributed among these distances:
  14   16  0.55
  15    4  0.14
  16    9  0.31

ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64


Consensus pattern (14 bp):   
ACTATTTTATTTTT

Found at i:813 original size:8 final size:8

Alignment explanation


    Indices: 790--822  Score: 52
    Period size: 8  Copynumber: 4.4  Consensus size: 8

        780 TATCCTTATA

                    
        790 ACTATTTT
          1 ACTATTTT

                    
        798 A-T-TTTT
          1 ACTATTTT

                    
        804 ACTATTTT
          1 ACTATTTT

                    
        812 ACTATTTT
          1 ACTATTTT

               
        820 ACT
          1 ACT

        823 TTTATAGTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
   6    5  0.22
   7    2  0.09
   8   16  0.70

ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64


Consensus pattern (8 bp):   
ACTATTTT

Found at i:818 original size:22 final size:22

Alignment explanation


    Indices: 790--836  Score: 69
    Period size: 22  Copynumber: 2.1  Consensus size: 22

        780 TATCCTTATA

                     *             
        790 ACTATTTTATTTTTACTA-TTTT
          1 ACTATTTTACTTTTA-TAGTTTT

                                  
        812 ACTATTTTACTTTTATAGTTTT
          1 ACTATTTTACTTTTATAGTTTT

               
        834 ACT
          1 ACT

        837 CAACTAAAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    2  0.09
  22   21  0.91

ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64


Consensus pattern (22 bp):   
ACTATTTTACTTTTATAGTTTT

Found at i:831 original size:93 final size:93

Alignment explanation


    Indices: 729--913  Score: 298
    Period size: 93  Copynumber: 2.0  Consensus size: 93

        719 TTATTTAAAT

                         *           *                  *           *        
        729 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTACATCTAATATCCTTATAACTA
          1 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCGTATAACTA

                        *  *      *     
        794 TTTTATTTTTACTATTTTACTATTTTAC
         66 TTTTATTTTTACAATATTACTAATTTAC

                                                                         *   
        822 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCGTATACCTA
          1 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCGTATAACTA

                                       
        887 TTTTATTTTTACAATATTACTAATTTA
         66 TTTTATTTTTACAATATTACTAATTTA

        914 ATTAAAAAGT


Statistics
Matches: 84,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  93   84  1.00

ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52


Consensus pattern (93 bp):   
TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCGTATAACTA
TTTTATTTTTACAATATTACTAATTTAC
Done.