Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008846.1 Corchorus capsularis cultivar CVL-1 contig08867, 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: 17692
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Found at i:13 original size:2 final size:2

Alignment explanation


    Indices: 7--59  Score: 81
    Period size: 2  Copynumber: 27.0  Consensus size: 2

          1 ATTCTA

                                                                          
          7 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

            *     *          
         48 GT AT GT AT AT AT
          1 AT AT AT AT AT AT

         60 GGTTTAATAG


Statistics
Matches: 46,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   45  0.98

ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51


Consensus pattern (2 bp):   
AT

Found at i:281 original size:132 final size:131

Alignment explanation


    Indices: 37--300  Score: 467
    Period size: 132  Copynumber: 2.0  Consensus size: 131

         27 ATATATATAT

                       *                      *       *                      
         37 ATATATTATATGTATGTATATATGGTTTAATAGATATTTTGATCCTTAAATTTGTAAGAAATGTA
          1 ATATATTATATATATGTATATATGGTTTAATAGACATTTTGACCCTTAAATTTGTAAGAAATGTA

                                                      *                      
        102 GAAATTAACTTTTAAACTTCTAAAATTGACAATTAAACGCTTGAATTTATTTTTCAAAAAAAATG
         66 GAAATTAACTTTTAAACTTCTAAAATTGACAATTAAACGCTTAAATTTATTTTT--AAAAAAATG

               
        167 AAA
        129 AAA

                                                                             
        170 ATATA-TATATATATGTATATATGGTTTAATAGACATTTTGACCCTTAAATTTGTAAGAAATGTA
          1 ATATATTATATATATGTATATATGGTTTAATAGACATTTTGACCCTTAAATTTGTAAGAAATGTA

                                                                             
        234 GAAATTAACTTTTAAACTTCTAAAATTGACAATTAAACGCTTAAATTTATTTTTAAAAAAATGAA
         66 GAAATTAACTTTTAAACTTCTAAAATTGACAATTAAACGCTTAAATTTATTTTTAAAAAAATGAA

             
        299 A
        131 A

             
        300 A
          1 A

        301 ATTAACGCTT


Statistics
Matches: 127,  Mismatches: 4, Indels: 3
        0.95            0.03        0.02

Matches are distributed among these distances:
 130   13  0.10
 132  109  0.86
 133    5  0.04

ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40


Consensus pattern (131 bp):   
ATATATTATATATATGTATATATGGTTTAATAGACATTTTGACCCTTAAATTTGTAAGAAATGTA
GAAATTAACTTTTAAACTTCTAAAATTGACAATTAAACGCTTAAATTTATTTTTAAAAAAATGAA
A

Found at i:1645 original size:20 final size:20

Alignment explanation


    Indices: 1620--1659  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1610 GTTTTAATAG

                                
       1620 TTTTCAAATTTTAAGTAACA
          1 TTTTCAAATTTTAAGTAACA

                   *            
       1640 TTTTCAAGTTTTAAGTAACA
          1 TTTTCAAATTTTAAGTAACA

       1660 CTATTCCCAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45


Consensus pattern (20 bp):   
TTTTCAAATTTTAAGTAACA

Found at i:10679 original size:2 final size:2

Alignment explanation


    Indices: 10672--10702  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      10662 AAATTATACA

                                                          
      10672 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 A

      10703 ATGATTTGCA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:12288 original size:2 final size:2

Alignment explanation


    Indices: 12283--12313  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      12273 ATATATATAT

                                                          
      12283 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G

      12314 TATTTGCAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
GA

Found at i:12757 original size:9 final size:9

Alignment explanation


    Indices: 12745--12770  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

      12735 TTTCTTTCTT

                     
      12745 TATTTCCTA
          1 TATTTCCTA

                     
      12754 TATTTCCTA
          1 TATTTCCTA

                    
      12763 TATTTCCT
          1 TATTTCCT

      12771 CTCATCTCTC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58


Consensus pattern (9 bp):   
TATTTCCTA
Done.