Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016367.1 Corchorus capsularis cultivar CVL-1 contig16388, 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: 23776
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31


Found at i:4054 original size:27 final size:28

Alignment explanation


    Indices: 3986--4058  Score: 87
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       3976 GGGTCACCCA

                     *                  
       3986 GGGCATTTTGGTCATTTTTACATTCAGG
          1 GGGCATTTTCGTCATTTTTACATTCAGG

                     *           *   *   
       4014 GGGCATTTTTGTCATTCTTT-TATTTA-G
          1 GGGCATTTTCGTCATT-TTTACATTCAGG

                              
       4041 GGGCATTTTCGTCATTTT
          1 GGGCATTTTCGTCATTTT

       4059 GAGTCCACTC


Statistics
Matches: 40,  Mismatches: 4, Indels: 4
        0.83            0.08        0.08

Matches are distributed among these distances:
  26    2  0.05
  27   16  0.40
  28   19  0.47
  29    3  0.08

ACGTcount: A:0.15, C:0.14, G:0.22, T:0.49


Consensus pattern (28 bp):   
GGGCATTTTCGTCATTTTTACATTCAGG

Found at i:4414 original size:14 final size:14

Alignment explanation


    Indices: 4395--4428  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       4385 GCATATTAAC

                          
       4395 TTTAGTCCATTTAG
          1 TTTAGTCCATTTAG

                          
       4409 TTTAGTCCATTTAG
          1 TTTAGTCCATTTAG

            *     
       4423 ATTAGT
          1 TTTAGT

       4429 ATCATAGTTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50


Consensus pattern (14 bp):   
TTTAGTCCATTTAG

Found at i:4594 original size:20 final size:20

Alignment explanation


    Indices: 4569--4607  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4559 AAATACAAGG

                                
       4569 CATTTGATTTACAAATTGGA
          1 CATTTGATTTACAAATTGGA

                      *        
       4589 CATTTGATTTGCAAATTGG
          1 CATTTGATTTACAAATTGG

       4608 TGCTCTTTTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41


Consensus pattern (20 bp):   
CATTTGATTTACAAATTGGA

Found at i:5630 original size:12 final size:12

Alignment explanation


    Indices: 5613--5649  Score: 65
    Period size: 12  Copynumber: 3.1  Consensus size: 12

       5603 GTGACCATCA

                   *    
       5613 AGCCAAATAAGC
          1 AGCCAAACAAGC

                        
       5625 AGCCAAACAAGC
          1 AGCCAAACAAGC

                        
       5637 AGCCAAACAAGC
          1 AGCCAAACAAGC

             
       5649 A
          1 A

       5650 ACGATTACAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  12   24  1.00

ACGTcount: A:0.51, C:0.30, G:0.16, T:0.03


Consensus pattern (12 bp):   
AGCCAAACAAGC

Found at i:12513 original size:3 final size:3

Alignment explanation


    Indices: 12505--12547  Score: 86
    Period size: 3  Copynumber: 14.3  Consensus size: 3

      12495 CAAAATTTAT

                                                                     
      12505 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

      12548 ATATACTAAA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   40  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:21425 original size:83 final size:85

Alignment explanation


    Indices: 21253--21435  Score: 266
    Period size: 83  Copynumber: 2.2  Consensus size: 85

      21243 AATTCATATG

                             *                                               
      21253 AGATATATACTTAAAAGTTTCTAATATAACTAAGTTTTGTAATTAAAATAGTAAAAATAGTAAAA
          1 AGATAT-TA-TTAAAAGATTCTAATATAACTAAGTTTTGTAATTAAAATAGTAAAAATAGTAAAA

                    *             
      21318 ATAAAATATTTATAAAGAGATT
         64 ATAAAATAGTTATAAAGAGATT

                                                 *                   *       
      21340 AGATATTATTAAAA-ATTCTAATATATA-TAAGTTTTTTAATTAAAATAGT-AAAATGGTAAAAA
          1 AGATATTATTAAAAGATTCTAATATA-ACTAAGTTTTGTAATTAAAATAGTAAAAATAGTAAAAA

                                 
      21402 TAAAATAGTTATAAAGAGATT
         65 TAAAATAGTTATAAAGAGATT

                          
      21423 AGAT-TTAATTAAA
          1 AGATATT-ATTAAA

      21436 TAGAAATAAA


Statistics
Matches: 90,  Mismatches: 4, Indels: 8
        0.88            0.04        0.08

Matches are distributed among these distances:
  82    2  0.02
  83   42  0.47
  84   31  0.34
  85    7  0.08
  86    2  0.02
  87    6  0.07

ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37


Consensus pattern (85 bp):   
AGATATTATTAAAAGATTCTAATATAACTAAGTTTTGTAATTAAAATAGTAAAAATAGTAAAAAT
AAAATAGTTATAAAGAGATT
Done.