Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006921.1 Corchorus capsularis cultivar CVL-1 contig06942, 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: 5659
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33


Found at i:326 original size:33 final size:33

Alignment explanation


    Indices: 257--357  Score: 114
    Period size: 33  Copynumber: 3.1  Consensus size: 33

        247 TCTTCATCGA

                        *              * *** 
        257 CATCAGTAGCCCAAGTTTCTTCATTCAAAGGGT
          1 CATCAGTAGCCCCAGTTTCTTCATTCACATCCT

                                          *  
        290 CATCAGTAGCCCCAGTTTCTTCATTCACATTCT
          1 CATCAGTAGCCCCAGTTTCTTCATTCACATCCT

                   *  *                       
        323 CATCAGTTGCACCA-TTTCCTTCATTCACATCCT
          1 CATCAGTAGCCCCAGTTT-CTTCATTCACATCCT

              
        356 CA
          1 CA

        358 ACATTTGCAC


Statistics
Matches: 59,  Mismatches: 8, Indels: 2
        0.86            0.12        0.03

Matches are distributed among these distances:
  32    3  0.05
  33   56  0.95

ACGTcount: A:0.24, C:0.32, G:0.11, T:0.34


Consensus pattern (33 bp):   
CATCAGTAGCCCCAGTTTCTTCATTCACATCCT

Found at i:366 original size:33 final size:33

Alignment explanation


    Indices: 305--383  Score: 106
    Period size: 33  Copynumber: 2.4  Consensus size: 33

        295 GTAGCCCCAG

                           *    *            
        305 TTTCTTCATTCACATTCTCATCAGTTGCACCA-
          1 TTTCTTCATTCACATCCTCAACAGTTGCACCAC

                                    *      *  
        337 TTTCCTTCATTCACATCCTCAACATTTGCACGAC
          1 TTT-CTTCATTCACATCCTCAACAGTTGCACCAC

                         
        371 TTTCTTCATTCAC
          1 TTTCTTCATTCAC

        384 GGGATTTTCT


Statistics
Matches: 41,  Mismatches: 4, Indels: 3
        0.85            0.08        0.06

Matches are distributed among these distances:
  32    3  0.07
  33   35  0.85
  34    3  0.07

ACGTcount: A:0.22, C:0.33, G:0.05, T:0.41


Consensus pattern (33 bp):   
TTTCTTCATTCACATCCTCAACAGTTGCACCAC

Found at i:4517 original size:14 final size:14

Alignment explanation


    Indices: 4500--4544  Score: 63
    Period size: 14  Copynumber: 3.2  Consensus size: 14

       4490 ATGATTTTTA

                          
       4500 TTTCTTAACTGAAT
          1 TTTCTTAACTGAAT

                 *  * *   
       4514 TTTCTAAATTAAAT
          1 TTTCTTAACTGAAT

                          
       4528 TTTCTTAACTGAAT
          1 TTTCTTAACTGAAT

               
       4542 TTT
          1 TTT

       4545 AAAATAAAAC


Statistics
Matches: 25,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  14   25  1.00

ACGTcount: A:0.31, C:0.11, G:0.04, T:0.53


Consensus pattern (14 bp):   
TTTCTTAACTGAAT

Found at i:4518 original size:36 final size:36

Alignment explanation


    Indices: 4447--4515  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       4437 TCTTTATATC

                  *                             
       4447 TTAACTGATAATTTTTATTTCTTAACTGGAATTTCT
          1 TTAACTAATAATTTTTATTTCTTAACTGGAATTTCT

                     *                        
       4483 TTAACTAATGATTTTTATTTCTTAACT-GAATTT
          1 TTAACTAATAATTTTTATTTCTTAACTGGAATTT

       4516 TCTAAATTAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  35    6  0.19
  36   25  0.81

ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54


Consensus pattern (36 bp):   
TTAACTAATAATTTTTATTTCTTAACTGGAATTTCT

Found at i:4777 original size:18 final size:18

Alignment explanation


    Indices: 4750--4784  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       4740 CCAATTTGAC

                              
       4750 TTTAACCTTATACAAGAT
          1 TTTAACCTTATACAAGAT

                 *           
       4768 TTTAATCTTATACAAGA
          1 TTTAACCTTATACAAGA

       4785 CAAAGGACAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40


Consensus pattern (18 bp):   
TTTAACCTTATACAAGAT

Found at i:5504 original size:32 final size:32

Alignment explanation


    Indices: 5462--5644  Score: 246
    Period size: 32  Copynumber: 5.7  Consensus size: 32

       5452 AGGACGGCTG

                 *                 *         
       5462 TGCCAGGGCATGCCGCCCTC-CTGGGGAGGCA-
          1 TGCCACGGCATGCCGCCC-CACTAGGGAGGCAC

                            *     *          
       5493 TGGCCACGGCATGCCGTCCCACAAGGGAGGCAC
          1 T-GCCACGGCATGCCGCCCCACTAGGGAGGCAC

                                            
       5526 TGCCACGGCATGCCGCCCCACTAGGGAGGCAC
          1 TGCCACGGCATGCCGCCCCACTAGGGAGGCAC

                                            
       5558 TGCCACGGCATGCCGCCCCACTAGGGAGGCAC
          1 TGCCACGGCATGCCGCCCCACTAGGGAGGCAC

                  *                     *   
       5590 TGCCACAGCATGCCGCCCCACTAGGGAGTCAC
          1 TGCCACGGCATGCCGCCCCACTAGGGAGGCAC

            *                  *    
       5622 AGCCACGGC-TGGCCGCCCTACTA
          1 TGCCACGGCAT-GCCGCCCCACTA

       5645 AGGCGGCAAT


Statistics
Matches: 137,  Mismatches: 11, Indels: 7
        0.88            0.07        0.05

Matches are distributed among these distances:
  31    3  0.02
  32  133  0.97
  33    1  0.01

ACGTcount: A:0.19, C:0.39, G:0.31, T:0.11


Consensus pattern (32 bp):   
TGCCACGGCATGCCGCCCCACTAGGGAGGCAC

Done.