Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009048.1 Corchorus capsularis cultivar CVL-1 contig09069, 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: 8388
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35


Found at i:893 original size:2 final size:2

Alignment explanation


    Indices: 886--912  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

        876 TTATTCATCT

                                                    
        886 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

        913 TACAAATAAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:7514 original size:14 final size:14

Alignment explanation


    Indices: 7495--7593  Score: 62
    Period size: 14  Copynumber: 7.2  Consensus size: 14

       7485 TTTATTTTAT

                          
       7495 AAATTCTTTTAAGA
          1 AAATTCTTTTAAGA

                  **      
       7509 AAATTCAATTAAG-
          1 AAATTCTTTTAAGA

                 *     *  *
       7522 AAATTTTATTTTA-T
          1 AAATTCT-TTTAAGA

                          
       7536 AAATTCTTTTAAGA
          1 AAATTCTTTTAAGA

                  **      
       7550 AAATTCAGTTAAG-
          1 AAATTCTTTTAAGA

                 *     *  *
       7563 AAATTTTATTTTA-T
          1 AAATTCT-TTTAAGA

                          
       7577 AAATTCTTTTAAGA
          1 AAATTCTTTTAAGA

               
       7591 AAA
          1 AAA

       7594 ATTTAGTTAA


Statistics
Matches: 61,  Mismatches: 18, Indels: 12
        0.67            0.20        0.13

Matches are distributed among these distances:
  13   18  0.30
  14   43  0.70

ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44


Consensus pattern (14 bp):   
AAATTCTTTTAAGA

Found at i:7541 original size:41 final size:41

Alignment explanation


    Indices: 7484--7608  Score: 223
    Period size: 41  Copynumber: 3.0  Consensus size: 41

       7474 CGTGCGACTG

                                            *        
       7484 TTTTATTTTATAAATTCTTTTAAGAAAATTCAATTAAGAAA
          1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA

                                                     
       7525 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
          1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA

                                           *          
       7566 TTTTATTTTATAAATTCTTTTAAGAAAAATTTAGTTAAGAAA
          1 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA

             
       7608 T
          1 T

       7609 GAAATTTTGT


Statistics
Matches: 81,  Mismatches: 2, Indels: 1
        0.96            0.02        0.01

Matches are distributed among these distances:
  41   64  0.79
  42   17  0.21

ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47


Consensus pattern (41 bp):   
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
Done.