Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006393.1 Corchorus capsularis cultivar CVL-1 contig06414, 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: 2215
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Found at i:1976 original size:17 final size:16

Alignment explanation


    Indices: 1910--1980  Score: 58
    Period size: 17  Copynumber: 4.4  Consensus size: 16

       1900 TTTCCCAGAA

                     *       
       1910 AAAATAGAAGGAAAAA-
          1 AAAA-AGAAAGAAAAAG

             *              
       1926 AGAAAGAAAG-AAAAG
          1 AAAAAGAAAGAAAAAG

              *               
       1941 AAGAAGAATA-ATAAAAG
          1 AAAAAGAA-AGA-AAAAG

                             
       1958 AAAAAGAAAGAAAAGAG
          1 AAAAAGAAAGAAAA-AG

                  
       1975 AAAAAG
          1 AAAAAG

       1981 CAACGATGGT


Statistics
Matches: 44,  Mismatches: 5, Indels: 11
        0.73            0.08        0.18

Matches are distributed among these distances:
  14    4  0.09
  15   11  0.25
  16    8  0.18
  17   21  0.48

ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04


Consensus pattern (16 bp):   
AAAAAGAAAGAAAAAG

Found at i:2038 original size:25 final size:25

Alignment explanation


    Indices: 2004--2080  Score: 85
    Period size: 25  Copynumber: 3.3  Consensus size: 25

       1994 AAAAAGAGCC

                                     
       2004 ATGGTTTTCAAAAGGTTTTGATAAA
          1 ATGGTTTTCAAAAGGTTTTGATAAA

                         *    *     *
       2029 ATGGTTTTCAAAAAG---AG-T--C
          1 ATGGTTTTCAAAAGGTTTTGATAAA

                                     
       2048 ATGGTTTTCAAAAGGTTTTGATAAA
          1 ATGGTTTTCAAAAGGTTTTGATAAA

                    
       2073 ATGGTTTT
          1 ATGGTTTT

       2081 TTTTAAAAAG


Statistics
Matches: 40,  Mismatches: 6, Indels: 12
        0.69            0.10        0.21

Matches are distributed among these distances:
  19   14  0.35
  21    1  0.03
  22    2  0.05
  23    1  0.03
  25   22  0.55

ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40


Consensus pattern (25 bp):   
ATGGTTTTCAAAAGGTTTTGATAAA

Found at i:2040 original size:44 final size:44

Alignment explanation


    Indices: 1986--2128  Score: 225
    Period size: 44  Copynumber: 3.2  Consensus size: 44

       1976 AAAAGCAACG

                             *                          
       1986 ATGG-TTTCAAAAAGAGCCATGGTTTTCAAAAGGTTTTGATAAA
          1 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA

                                                        
       2029 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
          1 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA

                       *                      *            
       2073 ATGGTTTTTTTTAAAAAGAGTCATGGTTTTCAAAGGGTTTTGATAAA
          1 ATGG---TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA

                     
       2120 ATGGTTTTC
          1 ATGGTTTTC

       2129 CAAAGTTGTG


Statistics
Matches: 92,  Mismatches: 4, Indels: 7
        0.89            0.04        0.07

Matches are distributed among these distances:
  43    4  0.04
  44   46  0.50
  47   42  0.46

ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38


Consensus pattern (44 bp):   
ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA

Found at i:2112 original size:47 final size:47

Alignment explanation


    Indices: 1990--2127  Score: 228
    Period size: 47  Copynumber: 3.0  Consensus size: 47

       1980 GCAACGATGG

                        *                                  
       1990 TTTCAAAAAGAGCCATGGTTTTCAAAAGGTTTTGATAAAATGG---T
          1 TTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTTTT

                                                           
       2034 TTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTTTT
          1 TTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTTTT

               *                      *                    
       2081 TTTTAAAAAGAGTCATGGTTTTCAAAGGGTTTTGATAAAATGGTTTT
          1 TTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTTTT

       2128 CCAAAGTTGT


Statistics
Matches: 88,  Mismatches: 3, Indels: 3
        0.94            0.03        0.03

Matches are distributed among these distances:
  44   42  0.48
  47   46  0.52

ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39


Consensus pattern (47 bp):   
TTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTTTT
Done.