Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012530.1 Corchorus capsularis cultivar CVL-1 contig12551, 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: 14399
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32


Found at i:6352 original size:22 final size:22

Alignment explanation


    Indices: 6327--6422  Score: 92
    Period size: 22  Copynumber: 4.5  Consensus size: 22

       6317 ACAATACTCG

                                  
       6327 AAATTTCATAGTGTGATTATCA
          1 AAATTTCATAGTGTGATTATCA

                   *    *      *  
       6349 AAATTTCGTAG-ATG-TTAACA
          1 AAATTTCATAGTGTGATTATCA

             *             *        
       6369 AGATTTC--AGTGTATAGTTATCA
          1 AAATTTCATAGTGT-GA-TTATCA

                      *           
       6391 AAATTTCATAATGTGATTATCA
          1 AAATTTCATAGTGTGATTATCA

                      
       6413 AAATTTCATA
          1 AAATTTCATA

       6423 AGAATATTTA


Statistics
Matches: 58,  Mismatches: 10, Indels: 12
        0.73            0.12        0.15

Matches are distributed among these distances:
  18    2  0.03
  19    1  0.02
  20   11  0.19
  21    2  0.03
  22   37  0.64
  23    1  0.02
  24    4  0.07

ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40


Consensus pattern (22 bp):   
AAATTTCATAGTGTGATTATCA

Found at i:6526 original size:13 final size:14

Alignment explanation


    Indices: 6502--6530  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

       6492 CATAAAAATT

                          
       6502 AAAATTAGTAATAA
          1 AAAATTAGTAATAA

                          
       6516 AAAATTA-TAATAA
          1 AAAATTAGTAATAA

              
       6529 AA
          1 AA

       6531 GAAAAAAAGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    8  0.53
  14    7  0.47

ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28


Consensus pattern (14 bp):   
AAAATTAGTAATAA

Found at i:7411 original size:31 final size:30

Alignment explanation


    Indices: 7340--7430  Score: 76
    Period size: 31  Copynumber: 3.0  Consensus size: 30

       7330 GTCCATTAGC

                                **    *    
       7340 TTTTAATTTGTTTAATTTAAGGCTTGCATTT
          1 TTTTAATTTGTTTAATTTAATACTT-AATTT

             ** *                         
       7371 TGATGATTTGTTTAATTTAATACTTAATTT
          1 TTTTAATTTGTTTAATTTAATACTTAATTT

                         **                
       7401 GTTTTAATTTGCTACAATTTAATA-TTAATT
          1 -TTTTAATTTG-TTTAATTTAATACTTAATT

       7431 AGCATTAAAT


Statistics
Matches: 47,  Mismatches: 11, Indels: 4
        0.76            0.18        0.06

Matches are distributed among these distances:
  30    4  0.09
  31   33  0.70
  32   10  0.21

ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56


Consensus pattern (30 bp):   
TTTTAATTTGTTTAATTTAATACTTAATTT

Found at i:7946 original size:23 final size:23

Alignment explanation


    Indices: 7916--7971  Score: 76
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       7906 TATCAAAAGT

                              *    
       7916 GAACCCGAACCCGACCCGGGCCC
          1 GAACCCGAACCCGACCCGAGCCC

                       *  *        
       7939 GAACCCGAACCTGATCCGAGCCC
          1 GAACCCGAACCCGACCCGAGCCC

                      
       7962 GAAACCCGAA
          1 G-AACCCGAA

       7972 AATACCCGAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  23   21  0.72
  24    8  0.28

ACGTcount: A:0.29, C:0.45, G:0.23, T:0.04


Consensus pattern (23 bp):   
GAACCCGAACCCGACCCGAGCCC

Found at i:8026 original size:15 final size:16

Alignment explanation


    Indices: 7963--8031  Score: 77
    Period size: 16  Copynumber: 4.4  Consensus size: 16

       7953 TCCGAGCCCG

                            
       7963 AAACCCGAAAATACCC
          1 AAACCCGAAAATACCC

            *         *    *
       7979 GAACCCGAAAGTACCT
          1 AAACCCGAAAATACCC

            *   *           
       7995 GAACTCGAAAATACCC
          1 AAACCCGAAAATACCC

                      *     
       8011 AAACCCG-AAGTACCC
          1 AAACCCGAAAATACCC

                  
       8026 AAACCC
          1 AAACCC

       8032 ACCCGAACCT


Statistics
Matches: 44,  Mismatches: 9, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  15   13  0.30
  16   31  0.70

ACGTcount: A:0.43, C:0.36, G:0.12, T:0.09


Consensus pattern (16 bp):   
AAACCCGAAAATACCC
Done.