Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007047.1 Corchorus capsularis cultivar CVL-1 contig07068, 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: 25386
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35


Found at i:8053 original size:33 final size:33

Alignment explanation


    Indices: 8016--8091  Score: 116
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       8006 TTCTTTTCAC

                     **      *               
       8016 CCAAAACAGTCCTATTTTCAATGCTATGATCAA
          1 CCAAAACAGAACTATTTGCAATGCTATGATCAA

                       *                     
       8049 CCAAAACAGAATTATTTGCAATGCTATGATCAA
          1 CCAAAACAGAACTATTTGCAATGCTATGATCAA

                      
       8082 CCAAAACAGA
          1 CCAAAACAGA

       8092 TTTAGTTTCA


Statistics
Matches: 39,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  33   39  1.00

ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25


Consensus pattern (33 bp):   
CCAAAACAGAACTATTTGCAATGCTATGATCAA

Found at i:8120 original size:33 final size:33

Alignment explanation


    Indices: 8083--8188  Score: 110
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       8073 TATGATCAAC

                           *                   
       8083 CAAAACAGATTTAGTTTCA-T-CATACACAACACT
          1 CAAAACAGATTTAGTGTCATTGCA-A-ACAACACT

                                             
       8116 CAAAACAGATTTAGTGTCATTGCAAACAACACT
          1 CAAAACAGATTTAGTGTCATTGCAAACAACACT

                **  *      *    *            
       8149 CAAATTAGGTTTAGTATCATCGCAAACAACA-T
          1 CAAAACAGATTTAGTGTCATTGCAAACAACACT

                    
       8181 CTAAAACA
          1 C-AAAACA

       8189 CTCTTTGCAA


Statistics
Matches: 62,  Mismatches: 8, Indels: 6
        0.82            0.11        0.08

Matches are distributed among these distances:
  32    2  0.03
  33   56  0.90
  34    2  0.03
  35    2  0.03

ACGTcount: A:0.43, C:0.22, G:0.09, T:0.25


Consensus pattern (33 bp):   
CAAAACAGATTTAGTGTCATTGCAAACAACACT

Found at i:12072 original size:52 final size:52

Alignment explanation


    Indices: 11993--12092  Score: 173
    Period size: 52  Copynumber: 1.9  Consensus size: 52

      11983 GAATTTCAGA

                         *        *                             
      11993 ACAACTTCGGCCCTGAACTTGTTCAACTTCGGGACAGAAGTTATTGCGCAAG
          1 ACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTATTGCGCAAG

                                                      *     
      12045 ACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTGTTGCG
          1 ACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTATTGCG

      12093 GGAAAAACCT


Statistics
Matches: 45,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  52   45  1.00

ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24


Consensus pattern (52 bp):   
ACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTATTGCGCAAG

Found at i:12082 original size:22 final size:22

Alignment explanation


    Indices: 12045--12088  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      12035 ATTGCGCAAG

                       *          
      12045 ACAACTTCGGCCCAGAACTTGT
          1 ACAACTTCGGCACAGAACTTGT

                      *      *    
      12067 ACAACTTCGGGACAGAAGTTGT
          1 ACAACTTCGGCACAGAACTTGT

      12089 TGCGGGAAAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23


Consensus pattern (22 bp):   
ACAACTTCGGCACAGAACTTGT

Found at i:13865 original size:12 final size:12

Alignment explanation


    Indices: 13848--13897  Score: 64
    Period size: 12  Copynumber: 4.2  Consensus size: 12

      13838 AAAAATAAGA

                        
      13848 GAATAAAATTTG
          1 GAATAAAATTTG

                  *     
      13860 GAATAAGATTTG
          1 GAATAAAATTTG

                   *    
      13872 GAATAAACTTTG
          1 GAATAAAATTTG

                *  *    
      13884 GAATGAACTTTG
          1 GAATAAAATTTG

              
      13896 GA
          1 GA

      13898 GAAAATTTCT


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   34  1.00

ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32


Consensus pattern (12 bp):   
GAATAAAATTTG

Found at i:18663 original size:26 final size:26

Alignment explanation


    Indices: 18627--18690  Score: 67
    Period size: 28  Copynumber: 2.4  Consensus size: 26

      18617 ATCAAAGTTT

                                       
      18627 AAAAGAAAATAA-AAAAAAAGAAGAAA
          1 AAAAGAAAATAAGAAAAAAA-AAGAAA

                  *               *    
      18653 AAAAGAGAATAATGAAAAAAAATGAAA
          1 AAAAGAAAATAA-GAAAAAAAAAGAAA

               *       
      18680 AATCAGAAAAT
          1 AA-AAGAAAAT

      18691 CAAAAGAGGT


Statistics
Matches: 31,  Mismatches: 4, Indels: 4
        0.79            0.10        0.10

Matches are distributed among these distances:
  26   11  0.35
  27    7  0.23
  28   13  0.42

ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09


Consensus pattern (26 bp):   
AAAAGAAAATAAGAAAAAAAAAGAAA

Found at i:25350 original size:2 final size:2

Alignment explanation


    Indices: 25343--25372  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      25333 TAACAACAAT

                                                        
      25343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      25373 AGATAGCAAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.