Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015722.1 Corchorus capsularis cultivar CVL-1 contig15743, 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: 15320
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:483 original size:51 final size:51

Alignment explanation


    Indices: 397--565  Score: 225
    Period size: 51  Copynumber: 3.3  Consensus size: 51

        387 CAAAACTATC

                     *            *   *  * *             *      
        397 AAGATTCAACTTTTATTG-TTAGAATTACAAAAACTCAACCCTTATTACATA
          1 AAGATTCAATTTTTA-TGATTAAAATCACTAGAACTCAACCCTTACTACATA

                                                                
        448 AAGATAT-AATTTTTATGATTAAAATCACTAGAACTCAACCCTTACTACATA
          1 AAGAT-TCAATTTTTATGATTAAAATCACTAGAACTCAACCCTTACTACATA

                             *                      *      *   
        499 AAGATTCAATTTTTATGGTTAAAATCACTAGAACTCAACCTTTACTATATA
          1 AAGATTCAATTTTTATGATTAAAATCACTAGAACTCAACCCTTACTACATA

                            
        550 AAGATTCAATTTTTAT
          1 AAGATTCAATTTTTAT

        566 TTGCCAAAAA


Statistics
Matches: 106,  Mismatches: 9, Indels: 6
        0.88            0.07        0.05

Matches are distributed among these distances:
  50    3  0.03
  51  102  0.96
  52    1  0.01

ACGTcount: A:0.41, C:0.16, G:0.07, T:0.37


Consensus pattern (51 bp):   
AAGATTCAATTTTTATGATTAAAATCACTAGAACTCAACCCTTACTACATA

Found at i:5474 original size:56 final size:56

Alignment explanation


    Indices: 5408--5523  Score: 232
    Period size: 56  Copynumber: 2.1  Consensus size: 56

       5398 AGTGATGTTC

                                                                    
       5408 GAGATCATGCATCCACCGATACCTATGTAACTACGCATATGAGCATTTGGAAGCTG
          1 GAGATCATGCATCCACCGATACCTATGTAACTACGCATATGAGCATTTGGAAGCTG

                                                                    
       5464 GAGATCATGCATCCACCGATACCTATGTAACTACGCATATGAGCATTTGGAAGCTG
          1 GAGATCATGCATCCACCGATACCTATGTAACTACGCATATGAGCATTTGGAAGCTG

                
       5520 GAGA
          1 GAGA

       5524 GGACTTTGCT


Statistics
Matches: 60,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  56   60  1.00

ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24


Consensus pattern (56 bp):   
GAGATCATGCATCCACCGATACCTATGTAACTACGCATATGAGCATTTGGAAGCTG

Found at i:5603 original size:30 final size:29

Alignment explanation


    Indices: 5550--5626  Score: 84
    Period size: 30  Copynumber: 2.6  Consensus size: 29

       5540 TTAGAAGCTG

                         **               
       5550 GGGGCTTTGGAAGAAGGGAAGGACTTTGCT
          1 GGGGCTTTGGAAGCTGGGAAGGACTTTG-T

                                          
       5580 GGGGCTTTGGAAGCT-GGAGAGGACTTTGT
          1 GGGGCTTTGGAAGCTGGGA-AGGACTTTGT

            *   *   *         
       5609 TGGGATTTAGAAGCTGGG
          1 GGGGCTTTGGAAGCTGGG

       5627 GCTTTGGAAG


Statistics
Matches: 40,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  29   16  0.40
  30   24  0.60

ACGTcount: A:0.21, C:0.09, G:0.44, T:0.26


Consensus pattern (29 bp):   
GGGGCTTTGGAAGCTGGGAAGGACTTTGT

Found at i:5647 original size:74 final size:76

Alignment explanation


    Indices: 5509--5675  Score: 275
    Period size: 74  Copynumber: 2.2  Consensus size: 76

       5499 CATATGAGCA

                                                                             
       5509 TTTGGAAGCTGGAGAGGACTTTGCTGGGGATTTAGAAGCTGGGGGCTTTGGAAGAAGGGAAGGAC
          1 TTTGGAAGCTGGAGAGGACTTTGCTGGGGATTTAGAAGCTGGGGGCTTTGGAAGAAGGGAAGGAC

                  *    
       5574 TTTGCTGGGGC
         66 TTTGCTAGGGC

                                     *                             *         
       5585 TTTGGAAGCTGGAGAGGACTTTG-TTGGGATTTAGAAGCT-GGGGCTTTGGAAGATGGGAAGGAC
          1 TTTGGAAGCTGGAGAGGACTTTGCTGGGGATTTAGAAGCTGGGGGCTTTGGAAGAAGGGAAGGAC

                       
       5648 TTTGCTAGGGC
         66 TTTGCTAGGGC

               *      *      
       5659 TTTCGAAGCTAGAGAGG
          1 TTTGGAAGCTGGAGAGG

       5676 TAACTATTTC


Statistics
Matches: 86,  Mismatches: 5, Indels: 2
        0.92            0.05        0.02

Matches are distributed among these distances:
  74   48  0.56
  75   15  0.17
  76   23  0.27

ACGTcount: A:0.22, C:0.10, G:0.41, T:0.26


Consensus pattern (76 bp):   
TTTGGAAGCTGGAGAGGACTTTGCTGGGGATTTAGAAGCTGGGGGCTTTGGAAGAAGGGAAGGAC
TTTGCTAGGGC
Done.