Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021637.1 Corchorus olitorius cultivar O-4 contig21670, 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: 13333
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:53 original size:30 final size:30

Alignment explanation


    Indices: 17--77  Score: 106
    Period size: 30  Copynumber: 2.0  Consensus size: 30

          7 TTTTTGATTG

                                           
         17 ATTTGTAAATAAAGA-TGAAGTCTTTAAGTA
          1 ATTTGTAAATAAAGATTGAA-TCTTTAAGTA

                                          
         47 ATTTGTAAATAAAGATTGAATCTTTAAGTA
          1 ATTTGTAAATAAAGATTGAATCTTTAAGTA

             
         77 A
          1 A

         78 AAGGTGAAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  30   26  0.87
  31    4  0.13

ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38


Consensus pattern (30 bp):   
ATTTGTAAATAAAGATTGAATCTTTAAGTA

Found at i:8927 original size:19 final size:17

Alignment explanation


    Indices: 8881--8927  Score: 51
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       8871 ATAGGAACAG

                             
       8881 AAGAGGGGAAAATCGAA
          1 AAGAGGGGAAAATCGAA

                *              
       8898 AAGAAGGGAAAGAT-GAGA
          1 AAGAGGGGAAA-ATCGA-A

                        
       8916 AGAGAGGGGAAA
          1 A-AGAGGGGAAA

       8928 TAAGGAATCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  17   12  0.48
  18    4  0.16
  19    9  0.36

ACGTcount: A:0.53, C:0.02, G:0.40, T:0.04


Consensus pattern (17 bp):   
AAGAGGGGAAAATCGAA

Found at i:9939 original size:21 final size:22

Alignment explanation


    Indices: 9915--9958  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       9905 CATCTTGAAG

                                  
       9915 ATTTTAAAG-CCATCGGAGATC
          1 ATTTTAAAGCCCATCGGAGATC

                 *        *       
       9936 A-TTTGAAGCCCATTGGAGATC
          1 ATTTTAAAGCCCATCGGAGATC

              
       9957 AT
          1 AT

       9959 CAACAAAGGA


Statistics
Matches: 19,  Mismatches: 2, Indels: 3
        0.79            0.08        0.12

Matches are distributed among these distances:
  20    6  0.32
  21   13  0.68

ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30


Consensus pattern (22 bp):   
ATTTTAAAGCCCATCGGAGATC
Done.