Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006548.1 Corchorus capsularis cultivar CVL-1 contig06569, 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: 12972
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31


Found at i:4860 original size:19 final size:18

Alignment explanation


    Indices: 4836--4871  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4826 GAAGAATTAT

                               
       4836 TTGAAGACAATTTGAAGAC
          1 TTGAAGACAA-TTGAAGAC

                    *        
       4855 TTGAAGACTATTGAAGA
          1 TTGAAGACAATTGAAGA

       4872 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAC

Found at i:5505 original size:9 final size:9

Alignment explanation


    Indices: 5465--5507  Score: 50
    Period size: 10  Copynumber: 4.4  Consensus size: 9

       5455 ACTCTTATCA

                      
       5465 TTTTACTCGT
          1 TTTTACTC-T

                      
       5475 TTCTTACTCT
          1 TT-TTACTCT

             *        
       5485 TCTTACTACT
          1 TTTTACT-CT

                     
       5495 TTTTACTCT
          1 TTTTACTCT

                
       5504 TTTT
          1 TTTT

       5508 CTTTCTTATA


Statistics
Matches: 29,  Mismatches: 2, Indels: 5
        0.81            0.06        0.14

Matches are distributed among these distances:
   9   11  0.38
  10   12  0.41
  11    6  0.21

ACGTcount: A:0.12, C:0.23, G:0.02, T:0.63


Consensus pattern (9 bp):   
TTTTACTCT

Found at i:5568 original size:21 final size:20

Alignment explanation


    Indices: 5544--5641  Score: 106
    Period size: 21  Copynumber: 4.7  Consensus size: 20

       5534 TCTTTGAATC

                  *              
       5544 ACTGATCACCTTTTACTCTTT
          1 ACTGATTACCTTTTACTC-TT

                      *          
       5565 ACTGATTACTATTTTACTCTT
          1 ACTGATTAC-CTTTTACTCTT

             * *           *     
       5586 ATTAATTACCATTTTGCTCTT
          1 ACTGATTACC-TTTTACTCTT

                      *          
       5607 ACTGATTACTATTTTACTCTT
          1 ACTGATTAC-CTTTTACTCTT

                          
       5628 ACTGATTACCTTTT
          1 ACTGATTACCTTTT

       5642 TTAATCAGAA


Statistics
Matches: 63,  Mismatches: 11, Indels: 7
        0.78            0.14        0.09

Matches are distributed among these distances:
  20    4  0.06
  21   51  0.81
  22    8  0.13

ACGTcount: A:0.22, C:0.21, G:0.05, T:0.51


Consensus pattern (20 bp):   
ACTGATTACCTTTTACTCTT

Found at i:5609 original size:42 final size:43

Alignment explanation


    Indices: 5554--5642  Score: 135
    Period size: 42  Copynumber: 2.1  Consensus size: 43

       5544 ACTGATCACC

                                             *         
       5554 TTTTACTCTTTACTGATTACTATTTTACTCTTATTAATTACCA
          1 TTTTACTCTTTACTGATTACTATTTTACTCTTACTAATTACCA

                *                              *      *
       5597 TTTTGCTC-TTACTGATTACTATTTTACTCTTACTGATTACCT
          1 TTTTACTCTTTACTGATTACTATTTTACTCTTACTAATTACCA

                
       5639 TTTT
          1 TTTT

       5643 TAATCAGAAA


Statistics
Matches: 42,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  42   35  0.83
  43    7  0.17

ACGTcount: A:0.21, C:0.19, G:0.04, T:0.55


Consensus pattern (43 bp):   
TTTTACTCTTTACTGATTACTATTTTACTCTTACTAATTACCA

Found at i:5694 original size:35 final size:35

Alignment explanation


    Indices: 5655--5862  Score: 224
    Period size: 35  Copynumber: 5.9  Consensus size: 35

       5645 ATCAGAAAAC

                      *     *           *      
       5655 TAGGTAAAGATAGACTAGCTTAATTTCATGGAAAT
          1 TAGGTAAAGAAAGACTGGCTTAATTTCAAGGAAAT

                      *   *                *   
       5690 TAGGTAAAGATAGAGTGGCTTAATTTCAAGGGAAT
          1 TAGGTAAAGAAAGACTGGCTTAATTTCAAGGAAAT

              *                    *           *
       5725 TAAGTAAA-AAAGGACTGGCTTAGTTTCAAGGAAAC
          1 TAGGTAAAGAAA-GACTGGCTTAATTTCAAGGAAAT

                      *         *                
       5760 TAGGTAAAAAAAAAGACTGGTTTAATTTCAAGGAAAT
          1 TAGGT--AAAGAAAGACTGGCTTAATTTCAAGGAAAT

                                                
       5797 TAGGTAAAGGAAAGACTGGCTTAATTTCAAGGAAAT
          1 TAGGTAAA-GAAAGACTGGCTTAATTTCAAGGAAAT

              *              *              
       5833 TAAGT-AA-AAAGACAGAGGCTTAATTTCAAG
          1 TAGGTAAAGAAAGAC--TGGCTTAATTTCAAG

       5863 AAAGGAAATT


Statistics
Matches: 148,  Mismatches: 18, Indels: 14
        0.82            0.10        0.08

Matches are distributed among these distances:
  33    6  0.04
  34    2  0.01
  35   80  0.54
  36   29  0.20
  37   28  0.19
  38    3  0.02

ACGTcount: A:0.43, C:0.08, G:0.23, T:0.26


Consensus pattern (35 bp):   
TAGGTAAAGAAAGACTGGCTTAATTTCAAGGAAAT

Found at i:5915 original size:32 final size:32

Alignment explanation


    Indices: 5864--5935  Score: 108
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       5854 AATTTCAAGA

                *   *                       
       5864 AAGGAAATTAAGTAAAATAAAGAACTTAATTC
          1 AAGGTAATAAAGTAAAATAAAGAACTTAATTC

             *            *                 
       5896 AGGGTAATAAAGTAGAATAAAGAACTTAATTC
          1 AAGGTAATAAAGTAAAATAAAGAACTTAATTC

                    
       5928 AAGGTAAT
          1 AAGGTAAT

       5936 TTTTTTTGGC


Statistics
Matches: 35,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  32   35  1.00

ACGTcount: A:0.53, C:0.06, G:0.17, T:0.25


Consensus pattern (32 bp):   
AAGGTAATAAAGTAAAATAAAGAACTTAATTC
Done.