Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004249.1 Corchorus capsularis cultivar CVL-1 contig04257, 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: 3404
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:19 original size:13 final size:13

Alignment explanation


    Indices: 2--26  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

          1 T

                         
          2 TTTTTTTTTTTAG
          1 TTTTTTTTTTTAG

                        
         15 TTTTTTTTTTTA
          1 TTTTTTTTTTTA

         27 ATGTTCGATC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88


Consensus pattern (13 bp):   
TTTTTTTTTTTAG

Found at i:2325 original size:9 final size:9

Alignment explanation


    Indices: 2311--2335  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

       2301 TTTGTCCTTG

                     
       2311 CCGCCGCTA
          1 CCGCCGCTA

                     
       2320 CCGCCGCTA
          1 CCGCCGCTA

                   
       2329 CCGCCGC
          1 CCGCCGC

       2336 CACGGCCTCC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.08, C:0.60, G:0.24, T:0.08


Consensus pattern (9 bp):   
CCGCCGCTA

Found at i:3329 original size:33 final size:32

Alignment explanation


    Indices: 3258--3343  Score: 95
    Period size: 33  Copynumber: 2.6  Consensus size: 32

       3248 CCGTGGCGAA

                           *                
       3258 GCCGCCCCACTGGGGAGGC-TCAACCTCGGCG
          1 GCCGCCCCACTGGGGCGGCTTCAACCTCGGCG

                                          *     
       3289 GAACCGCCCCACTGGGGCGGCTTC-ACCATGGGCAG
          1 G--CCGCCCCACTGGGGCGGCTTCAACC-TCGGC-G

                     *          
       3324 GCCGCCCCATTGGGGCGGCT
          1 GCCGCCCCACTGGGGCGGCT

       3344 CGGCTATTTT


Statistics
Matches: 47,  Mismatches: 3, Indels: 8
        0.81            0.05        0.14

Matches are distributed among these distances:
  31    1  0.02
  33   38  0.81
  34    6  0.13
  35    2  0.04

ACGTcount: A:0.13, C:0.40, G:0.36, T:0.12


Consensus pattern (32 bp):   
GCCGCCCCACTGGGGCGGCTTCAACCTCGGCG
Done.