Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016405.1 Corchorus capsularis cultivar CVL-1 contig16426, 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: 8240
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35


Found at i:3619 original size:2 final size:2

Alignment explanation


    Indices: 3614--3638  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       3604 AGTAATACTA

                                                 
       3614 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       3639 AAATTTACTC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:4126 original size:77 final size:76

Alignment explanation


    Indices: 3966--4128  Score: 211
    Period size: 77  Copynumber: 2.1  Consensus size: 76

       3956 ATTATTTGAT

                *                          *     *     *                     
       3966 AAAAGAACTCTATATTTATTTAATTAAATCTGATATCTTTATAGCAAATTTTTTTACCATTTTAC
          1 AAAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACAAATTTTTTTACCATTTTAC

                   *   
       4031 TATTTTACTCA
         66 TATTTTAATCA

              *           *                                *                 
       4042 ACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC-TATTTTAGTTTACCATTT
          1 A-AAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACAAATTTT--TTTACCATTT

                        * 
       4106 TACTATTTTAATTA
         63 TACTATTTTAATCA

                     
       4120 AAAAAAACT
          1 AAAAAAACT

       4129 TGATATATTA


Statistics
Matches: 74,  Mismatches: 10, Indels: 5
        0.83            0.11        0.06

Matches are distributed among these distances:
  76    6  0.08
  77   45  0.61
  78   23  0.31

ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47


Consensus pattern (76 bp):   
AAAAAAACTCTATATTTATTTAATTAAATCTAATATCCTTATAACAAATTTTTTTACCATTTTAC
TATTTTAATCA

Found at i:7769 original size:14 final size:15

Alignment explanation


    Indices: 7740--7785  Score: 51
    Period size: 14  Copynumber: 3.2  Consensus size: 15

       7730 GGTTAGGGAA

                  *        
       7740 GAAGAAGAAG-AAAG
          1 GAAGAAAAAGAAAAG

              **           
       7754 GATTAAAAA-AAAAG
          1 GAAGAAAAAGAAAAG

                           
       7768 GAAGAAAAAGAAAAG
          1 GAAGAAAAAGAAAAG

               
       7783 GAA
          1 GAA

       7786 CACACTGTTT


Statistics
Matches: 25,  Mismatches: 5, Indels: 3
        0.76            0.15        0.09

Matches are distributed among these distances:
  14   17  0.68
  15    8  0.32

ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04


Consensus pattern (15 bp):   
GAAGAAAAAGAAAAG
Done.