Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001216.1 Corchorus capsularis cultivar CVL-1 contig01216, 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: 11186
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:6431 original size:42 final size:42

Alignment explanation


    Indices: 6367--6450  Score: 150
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       6357 AACGTAGAAT

                *        *                            
       6367 AACGTTAACATGCTGTATTTTGATGACGATTTAAGAAAAATG
          1 AACGATAACATGCCGTATTTTGATGACGATTTAAGAAAAATG

                                                      
       6409 AACGATAACATGCCGTATTTTGATGACGATTTAAGAAAAATG
          1 AACGATAACATGCCGTATTTTGATGACGATTTAAGAAAAATG

       6451 CAATTTTTGA


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   40  1.00

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


Consensus pattern (42 bp):   
AACGATAACATGCCGTATTTTGATGACGATTTAAGAAAAATG

Found at i:6668 original size:33 final size:33

Alignment explanation


    Indices: 6625--6741  Score: 171
    Period size: 33  Copynumber: 3.5  Consensus size: 33

       6615 AAATTTGTCT

                 *          *       *        
       6625 AGCCGCCCTAGTGGGGCGGCTCCGTCATGGCTG
          1 AGCCGTCCTAGTGGGGAGGCTCCGCCATGGCTG

                                        *    
       6658 AGCCGTCCTAGTGGGGAGGCTCCGCCATTGCTG
          1 AGCCGTCCTAGTGGGGAGGCTCCGCCATGGCTG

                                 *    *    * 
       6691 AGCCGTCCTAGTGGGGAGGCTTCGCCGTGGCGG
          1 AGCCGTCCTAGTGGGGAGGCTCCGCCATGGCTG

                              
       6724 AGCCGTCCTAGTGGGGAG
          1 AGCCGTCCTAGTGGGGAG

       6742 CCTCAGTGTA


Statistics
Matches: 76,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  33   76  1.00

ACGTcount: A:0.11, C:0.29, G:0.41, T:0.19


Consensus pattern (33 bp):   
AGCCGTCCTAGTGGGGAGGCTCCGCCATGGCTG

Found at i:6743 original size:16 final size:16

Alignment explanation


    Indices: 6690--6743  Score: 56
    Period size: 16  Copynumber: 3.3  Consensus size: 16

       6680 CGCCATTGCT

                            
       6690 GAGCCGTCCTAGTGGG
          1 GAGCCGTCCTAGTGGG

               * *     *      
       6706 GAGGCTTCGC-CGTGGCG
          1 GAGCCGTC-CTAGTGG-G

                            
       6723 GAGCCGTCCTAGTGGG
          1 GAGCCGTCCTAGTGGG

                 
       6739 GAGCC
          1 GAGCC

       6744 TCAGTGTAAA


Statistics
Matches: 29,  Mismatches: 6, Indels: 6
        0.71            0.15        0.15

Matches are distributed among these distances:
  16   17  0.59
  17   12  0.41

ACGTcount: A:0.11, C:0.28, G:0.44, T:0.17


Consensus pattern (16 bp):   
GAGCCGTCCTAGTGGG

Found at i:8541 original size:21 final size:21

Alignment explanation


    Indices: 8507--8547  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8497 ACTTCCTCAG

                 *   *           
       8507 CTTCATGCATATTCTCAGCTT
          1 CTTCAGGCAAATTCTCAGCTT

                           *    
       8528 CTTCAGGCAAATTCTGAGCT
          1 CTTCAGGCAAATTCTCAGCT

       8548 GCAGGCTCTA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.22, C:0.27, G:0.15, T:0.37


Consensus pattern (21 bp):   
CTTCAGGCAAATTCTCAGCTT
Done.