Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009644.1 Corchorus capsularis cultivar CVL-1 contig09665, 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: 9921
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:1139 original size:6 final size:6

Alignment explanation


    Indices: 1128--1154  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       1118 ACAAATAAAC

                                           
       1128 AAAGAA AAAGAA AAAGAA AAAGAA AAA
          1 AAAGAA AAAGAA AAAGAA AAAGAA AAA

       1155 CAGAGTCAGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00


Consensus pattern (6 bp):   
AAAGAA

Found at i:9182 original size:43 final size:43

Alignment explanation


    Indices: 9112--9209  Score: 169
    Period size: 43  Copynumber: 2.3  Consensus size: 43

       9102 AGGGTTAGTC

                 *                                     
       9112 ATAAATTTTAATACATTCCCCCATAGGATTTTAGAATAAAAAT
          1 ATAAAATTTAATACATTCCCCCATAGGATTTTAGAATAAAAAT

                              *   *                    
       9155 ATAAAATTTAATACATTCTCCCGTAGGATTTTAGAATAAAAAT
          1 ATAAAATTTAATACATTCCCCCATAGGATTTTAGAATAAAAAT

                        
       9198 ATAAAATTTAAT
          1 ATAAAATTTAAT

       9210 TTAACTAGGC


Statistics
Matches: 52,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  43   52  1.00

ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36


Consensus pattern (43 bp):   
ATAAAATTTAATACATTCCCCCATAGGATTTTAGAATAAAAAT

Found at i:9346 original size:40 final size:40

Alignment explanation


    Indices: 9302--9398  Score: 176
    Period size: 40  Copynumber: 2.4  Consensus size: 40

       9292 AAAAAATGGG

                                         *          
       9302 GGGATTGCTTACCATCTCCATCCATAACAGACAAGAAGAA
          1 GGGATTGCTTACCATCTCCATCCATAACAAACAAGAAGAA

                                                    
       9342 GGGATTGCTTACCATCTCCATCCATAACAAACAAGAAGAA
          1 GGGATTGCTTACCATCTCCATCCATAACAAACAAGAAGAA

              *              
       9382 GGAATTGCTTACCATCT
          1 GGGATTGCTTACCATCT

       9399 TCATAGACAA


Statistics
Matches: 55,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  40   55  1.00

ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23


Consensus pattern (40 bp):   
GGGATTGCTTACCATCTCCATCCATAACAAACAAGAAGAA

Done.