Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017120.1 Corchorus olitorius cultivar O-4 contig17153, 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: 7043
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:627 original size:15 final size:15

Alignment explanation


    Indices: 609--655  Score: 69
    Period size: 15  Copynumber: 3.2  Consensus size: 15

        599 GAAGGAGAGG

                           
        609 AGAAAAAAAAAGAAA
          1 AGAAAAAAAAAGAAA

                      *    
        624 AGAAAAAAAAGGAAA
          1 AGAAAAAAAAAGAAA

                    *      
        639 AG-AAAAAGAAGAAA
          1 AGAAAAAAAAAGAAA

               
        653 AGA
          1 AGA

        656 GCCACGCCAT


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  14   12  0.43
  15   16  0.57

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (15 bp):   
AGAAAAAAAAAGAAA

Found at i:631 original size:14 final size:14

Alignment explanation


    Indices: 612--655  Score: 70
    Period size: 14  Copynumber: 3.1  Consensus size: 14

        602 GGAGAGGAGA

                          
        612 AAAAAAAAGAAAAG
          1 AAAAAAAAGAAAAG

                           
        626 AAAAAAAAGGAAAAG
          1 AAAAAAAA-GAAAAG

                 *        
        641 AAAAAGAAGAAAAG
          1 AAAAAAAAGAAAAG

             
        655 A
          1 A

        656 GCCACGCCAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 2
        0.90            0.03        0.06

Matches are distributed among these distances:
  14   15  0.54
  15   13  0.46

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (14 bp):   
AAAAAAAAGAAAAG

Found at i:6663 original size:16 final size:17

Alignment explanation


    Indices: 6642--6673  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       6632 CATCTTGTAT

                             
       6642 AACTAAAC-AAAAAAAA
          1 AACTAAACTAAAAAAAA

                            
       6658 AACTAAACTAAAAAAA
          1 AACTAAACTAAAAAAA

       6674 TCTTTAGCTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    8  0.53
  17    7  0.47

ACGTcount: A:0.78, C:0.12, G:0.00, T:0.09


Consensus pattern (17 bp):   
AACTAAACTAAAAAAAA
Done.