Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013242.1 Corchorus capsularis cultivar CVL-1 contig13263, 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: 29078
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:190 original size:2 final size:2

Alignment explanation


    Indices: 134--172  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

        124 TTTTGTCTAG

                                                                      
        134 TA TA TA TA TA TA 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 TA TA TA TA TA TA T

        173 GAAAAATACA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:19807 original size:74 final size:74

Alignment explanation


    Indices: 19681--19826  Score: 265
    Period size: 74  Copynumber: 2.0  Consensus size: 74

      19671 GCTTCTTGAA

                *                                                            
      19681 CGGCTGCTTGTTCTTCCCCTTCTTCAGGGGCGACCCGTTCTCAGAGCAAAATCCCCCCATCCATG
          1 CGGCGGCTTGTTCTTCCCCTTCTTCAGGGGCGACCCGTTCTCAGAGCAAAATCCCCCCATCCATG

                     
      19746 CACCAAAAG
         66 CACCAAAAG

                                          *                      *           
      19755 CGGCGGCTTGTTCTTCCCCTTCTTCAGGGGTGACCCGTTCTCAGAGCAAAATCTCCCCATCCATG
          1 CGGCGGCTTGTTCTTCCCCTTCTTCAGGGGCGACCCGTTCTCAGAGCAAAATCCCCCCATCCATG

                   
      19820 CACCAAA
         66 CACCAAA

      19827 CTACAATCGA


Statistics
Matches: 69,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  74   69  1.00

ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24


Consensus pattern (74 bp):   
CGGCGGCTTGTTCTTCCCCTTCTTCAGGGGCGACCCGTTCTCAGAGCAAAATCCCCCCATCCATG
CACCAAAAG

Found at i:25557 original size:17 final size:17

Alignment explanation


    Indices: 25535--25572  Score: 76
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      25525 CCTCCGGTAT

                             
      25535 CTGATAACCACATTTAC
          1 CTGATAACCACATTTAC

                             
      25552 CTGATAACCACATTTAC
          1 CTGATAACCACATTTAC

                
      25569 CTGA
          1 CTGA

      25573 CTAATCCGGC


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

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29


Consensus pattern (17 bp):   
CTGATAACCACATTTAC
Done.