Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013075.1 Corchorus capsularis cultivar CVL-1 contig13096, 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: 6435
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38


Found at i:4536 original size:17 final size:17

Alignment explanation


    Indices: 4516--4549  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       4506 GTTTATAAAA

                             
       4516 AAACATTTTACGTACAT
          1 AAACATTTTACGTACAT

                      *      
       4533 AAACATTTTATGTACAT
          1 AAACATTTTACGTACAT

       4550 TAAAGCTGAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38


Consensus pattern (17 bp):   
AAACATTTTACGTACAT

Found at i:4584 original size:18 final size:20

Alignment explanation


    Indices: 4561--4612  Score: 63
    Period size: 21  Copynumber: 2.6  Consensus size: 20

       4551 AAAGCTGAAG

                            *   
       4561 TTATAACCTTA-A-TTTTTT
          1 TTATAACCTTATAGTTATTT

                                 
       4579 TTATAACCTCTATAGTTATTT
          1 TTATAACCT-TATAGTTATTT

                         
       4600 TTAGTAACCTTAT
          1 TTA-TAACCTTAT

       4613 TAGATGTGAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  18    9  0.31
  19    2  0.07
  20    1  0.03
  21   11  0.38
  22    6  0.21

ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54


Consensus pattern (20 bp):   
TTATAACCTTATAGTTATTT

Found at i:5480 original size:28 final size:28

Alignment explanation


    Indices: 5444--5500  Score: 96
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       5434 TCAATCTCTC

                *        *              
       5444 TTTCGTTTTATTTTACAATGGGGGGAGG
          1 TTTCATTTTATTTCACAATGGGGGGAGG

                                        
       5472 TTTCATTTTATTTCACAATGGGGGGAGG
          1 TTTCATTTTATTTCACAATGGGGGGAGG

             
       5500 T
          1 T

       5501 GGGATGGTAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   27  1.00

ACGTcount: A:0.19, C:0.09, G:0.30, T:0.42


Consensus pattern (28 bp):   
TTTCATTTTATTTCACAATGGGGGGAGG
Done.