Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001135.1 Corchorus capsularis cultivar CVL-1 contig01135, 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: 14558
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:2237 original size:2 final size:2

Alignment explanation


    Indices: 2230--2264  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       2220 ACCCCTCAAG

                         *                                      
       2230 TA TA TA TA TC 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 TA TA TA TA T

       2265 CATTCTTCAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:11463 original size:28 final size:29

Alignment explanation


    Indices: 11422--11480  Score: 102
    Period size: 28  Copynumber: 2.1  Consensus size: 29

      11412 TATGTAAAGT

                                         
      11422 TTGATGTCAAAAAAAAAGTATGATATGTG
          1 TTGATGTCAAAAAAAAAGTATGATATGTG

                                    *    
      11451 TTGATGTC-AAAAAAAAGTATGATCTGTG
          1 TTGATGTCAAAAAAAAAGTATGATATGTG

              
      11479 TT
          1 TT

      11481 AACATCAGAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  28   21  0.72
  29    8  0.28

ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34


Consensus pattern (29 bp):   
TTGATGTCAAAAAAAAAGTATGATATGTG

Found at i:14476 original size:2 final size:2

Alignment explanation


    Indices: 14469--14499  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      14459 CTCATGGTCA

                                                          
      14469 AT AT AT 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 AT AT AT A

      14500 GTAGGTAGGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AT

Done.