Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001195.1 Corchorus capsularis cultivar CVL-1 contig01195, 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: 11286
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:6430 original size:6 final size:6

Alignment explanation


    Indices: 6419--6447  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       6409 AACCTTTCCT

                                             
       6419 CCATGA CCATGA CCATGA CCATGA CCATG
          1 CCATGA CCATGA CCATGA CCATGA CCATG

       6448 TGAGAGGTGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17


Consensus pattern (6 bp):   
CCATGA

Found at i:8905 original size:43 final size:43

Alignment explanation


    Indices: 8857--8945  Score: 178
    Period size: 43  Copynumber: 2.1  Consensus size: 43

       8847 ATATTACTGT

                                                       
       8857 TAATAGAAGTGCATATTAGCTGAAGATTATTGTAACAACATTA
          1 TAATAGAAGTGCATATTAGCTGAAGATTATTGTAACAACATTA

                                                       
       8900 TAATAGAAGTGCATATTAGCTGAAGATTATTGTAACAACATTA
          1 TAATAGAAGTGCATATTAGCTGAAGATTATTGTAACAACATTA

               
       8943 TAA
          1 TAA

       8946 ACAGTTTAAT


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   46  1.00

ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33


Consensus pattern (43 bp):   
TAATAGAAGTGCATATTAGCTGAAGATTATTGTAACAACATTA

Found at i:10765 original size:5 final size:5

Alignment explanation


    Indices: 10759--10792  Score: 59
    Period size: 5  Copynumber: 6.8  Consensus size: 5

      10749 TCTCTATCAA

                *                                   
      10759 AAAAA AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
          1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA

      10793 TGATGTATTG


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   5   28  1.00

ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00


Consensus pattern (5 bp):   
AAAAC

Found at i:11172 original size:129 final size:132

Alignment explanation


    Indices: 10937--11197  Score: 420
    Period size: 129  Copynumber: 2.0  Consensus size: 132

      10927 ACTCATTATT

                                  *                                          
      10937 AACAGCTAAAAAACATAGGCTATCAACCACCCTAATAAAGTCCTTCTATGTCCTTGAGATGCATA
          1 AACAGCTAAAAAACATAGGCTACCAACCACCCTAATAAAGTCC-TC-ATGTCCTTGAGATGCATA

                                                        *       *  *    *    
      11002 TGAGAGCTGATTTCATGCAAAATTATGAAAGACATGGAAAGATAGAAGAAAAGGATAGCTTGAGC
         64 TGAGAGCTGATTTCATGCAAAATTATGAAAGACATGGAAAGATAAAAGAAAAAGACAGCTAGAGC

                
      11067 CTAG
        129 CTAG

                                                                        *    
      11071 AACAGCTAAAAAACATAGGCTACCAACCACCCTAATAAAGT-C-C-TGTCCTTGAGATGCGTATG
          1 AACAGCTAAAAAACATAGGCTACCAACCACCCTAATAAAGTCCTCATGTCCTTGAGATGCATATG

                                             *                               
      11133 AGAGCTGATTTCATGCAAAATTATGAAAGACATTGAAAGATAAAAGAAAAAGACAGCTAGAGCCT
         66 AGAGCTGATTTCATGCAAAATTATGAAAGACATGGAAAGATAAAAGAAAAAGACAGCTAGAGCCT

      11198 TGAAGATTAT


Statistics
Matches: 120,  Mismatches: 7, Indels: 5
        0.91            0.05        0.04

Matches are distributed among these distances:
 129   78  0.65
 131    1  0.01
 133    1  0.01
 134   40  0.33

ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Consensus pattern (132 bp):   
AACAGCTAAAAAACATAGGCTACCAACCACCCTAATAAAGTCCTCATGTCCTTGAGATGCATATG
AGAGCTGATTTCATGCAAAATTATGAAAGACATGGAAAGATAAAAGAAAAAGACAGCTAGAGCCT
AG
Done.