Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013561.1 Corchorus capsularis cultivar CVL-1 contig13582, 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: 13196
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30


Found at i:9738 original size:15 final size:15

Alignment explanation


    Indices: 9720--9748  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       9710 CTGCAAAATT

                           
       9720 AACAAAAACAAAAAA
          1 AACAAAAACAAAAAA

                          
       9735 AACAAAAACAAAAA
          1 AACAAAAACAAAAA

       9749 CAAAATACGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00


Consensus pattern (15 bp):   
AACAAAAACAAAAAA

Found at i:9749 original size:12 final size:11

Alignment explanation


    Indices: 9720--9770  Score: 52
    Period size: 12  Copynumber: 4.6  Consensus size: 11

       9710 CTGCAAAATT

                       
       9720 AACAAAAAC-A
          1 AACAAAAACAA

                        
       9730 AA-AAAAACAAA
          1 AACAAAAAC-AA

                       
       9741 AACAAAAACAA
          1 AACAAAAACAA

              *  *      
       9752 AATACGAAACAA
          1 AACA-AAAACAA

                   
       9764 AACAAAA
          1 AACAAAA

       9771 CTAAAGGAAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 7
        0.75            0.09        0.16

Matches are distributed among these distances:
   9    6  0.18
  10    2  0.06
  11   10  0.30
  12   15  0.45

ACGTcount: A:0.80, C:0.16, G:0.02, T:0.02


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:13171 original size:2 final size:2

Alignment explanation


    Indices: 13164--13196  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      13154 ATATAGTGAG

                                                             
      13164 AT 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 AT A


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
AT

Done.