Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014334.1 Corchorus capsularis cultivar CVL-1 contig14355, 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: 21334
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31


Found at i:4698 original size:46 final size:46

Alignment explanation


    Indices: 4645--4735  Score: 146
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       4635 CCAAGAAGAT

                                 **    *   *              
       4645 AAGTGCAACCTGATAGTACAATGTAAGTATGTGAGAATTTAGAACA
          1 AAGTGCAACCTGATAGTACAACATAAGCATGAGAGAATTTAGAACA

                                                         
       4691 AAGTGCAACCTGATAGTACAACATAAGCATGAGAGAATTTAGAAC
          1 AAGTGCAACCTGATAGTACAACATAAGCATGAGAGAATTTAGAAC

       4736 CAAATAAAAC


Statistics
Matches: 41,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  46   41  1.00

ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23


Consensus pattern (46 bp):   
AAGTGCAACCTGATAGTACAACATAAGCATGAGAGAATTTAGAACA

Found at i:8253 original size:18 final size:18

Alignment explanation


    Indices: 8230--8265  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       8220 TGTTATTACC

                              
       8230 ATTCTTCTTTCACTTCCA
          1 ATTCTTCTTTCACTTCCA

                  *           
       8248 ATTCTTTTTTCACTTCCA
          1 ATTCTTCTTTCACTTCCA

       8266 TTTGATTCAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.17, C:0.31, G:0.00, T:0.53


Consensus pattern (18 bp):   
ATTCTTCTTTCACTTCCA

Found at i:9479 original size:16 final size:16

Alignment explanation


    Indices: 9458--9490  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       9448 TTACTAATGT

                            
       9458 AACATAATTAAATTGA
          1 AACATAATTAAATTGA

                            
       9474 AACATAATTAAATTGA
          1 AACATAATTAAATTGA

             
       9490 A
          1 A

       9491 GCAACTTTTA


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

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30


Consensus pattern (16 bp):   
AACATAATTAAATTGA

Found at i:16404 original size:13 final size:13

Alignment explanation


    Indices: 16386--16426  Score: 64
    Period size: 13  Copynumber: 3.2  Consensus size: 13

      16376 GGTGACATCG

                         
      16386 GCATGGCATGGGT
          1 GCATGGCATGGGT

                         
      16399 GCATGGCATGGGT
          1 GCATGGCATGGGT

              *  *       
      16412 GCTTGTCATGGGT
          1 GCATGGCATGGGT

              
      16425 GC
          1 GC

      16427 TGTCCGCGCA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  13   26  1.00

ACGTcount: A:0.12, C:0.17, G:0.44, T:0.27


Consensus pattern (13 bp):   
GCATGGCATGGGT

Found at i:16495 original size:21 final size:21

Alignment explanation


    Indices: 16451--16496  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      16441 CCAGGGCACA

                         *     * 
      16451 TGGGTGCCCAGGCCAACCGGC
          1 TGGGTGCCCAGGCAAACCGCC

                   *        *    
      16472 TGGGTGCGCAGGCAAAGCGCC
          1 TGGGTGCCCAGGCAAACCGCC

                
      16493 TGGG
          1 TGGG

      16497 CGCATAGCCA


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.15, C:0.30, G:0.43, T:0.11


Consensus pattern (21 bp):   
TGGGTGCCCAGGCAAACCGCC
Done.