Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015328.1 Corchorus capsularis cultivar CVL-1 contig15349, 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: 17678
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:4254 original size:2 final size:2

Alignment explanation


    Indices: 4249--4280  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       4239 CATCATAATA

                                                           
       4249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       4281 TCTACGAAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:5884 original size:32 final size:32

Alignment explanation


    Indices: 5812--5885  Score: 87
    Period size: 32  Copynumber: 2.3  Consensus size: 32

       5802 CTGCCCCACC

                         *                  
       5812 GGGGCGGCCTGCCGTGGCGAAACCGCCCCAGG
          1 GGGGCGGCCTGCCCTGGCGAAACCGCCCCAGG

            *  *                 * *        
       5844 AGGACGGCCTGCCCTGGCGAAGCTGCCCC-GG
          1 GGGGCGGCCTGCCCTGGCGAAACCGCCCCAGG

                       
       5875 TGGGGCGGCCT
          1 -GGGGCGGCCT

       5886 TTTCAGCCCC


Statistics
Matches: 34,  Mismatches: 7, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  31    2  0.06
  32   32  0.94

ACGTcount: A:0.11, C:0.36, G:0.43, T:0.09


Consensus pattern (32 bp):   
GGGGCGGCCTGCCCTGGCGAAACCGCCCCAGG

Found at i:6480 original size:37 final size:37

Alignment explanation


    Indices: 6439--6516  Score: 156
    Period size: 37  Copynumber: 2.1  Consensus size: 37

       6429 TCTTAATTAT

                                                 
       6439 AAGCATCGTATATTGTTTTCCCCTTAACGAATAATCA
          1 AAGCATCGTATATTGTTTTCCCCTTAACGAATAATCA

                                                 
       6476 AAGCATCGTATATTGTTTTCCCCTTAACGAATAATCA
          1 AAGCATCGTATATTGTTTTCCCCTTAACGAATAATCA

                
       6513 AAGC
          1 AAGC

       6517 CAGATTTAGG


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   41  1.00

ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33


Consensus pattern (37 bp):   
AAGCATCGTATATTGTTTTCCCCTTAACGAATAATCA

Found at i:6556 original size:2 final size:2

Alignment explanation


    Indices: 6549--6574  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       6539 TTGCACTTTC

                                                  
       6549 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       6575 GGCATAAATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:6822 original size:53 final size:53

Alignment explanation


    Indices: 6737--6838  Score: 150
    Period size: 53  Copynumber: 1.9  Consensus size: 53

       6727 GACGTAGCAC

                 *                 ** *               *          
       6737 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACTAAAAAGCCGT
          1 GCCACATGTACCAAAAAGTGACACATAGCACGCCACATGTACCAAAAAGCCGT

                                       *                     
       6790 GCCACATGTACCAAAAAGTGACACATATCACGCCACATGTACCAAAAAG
          1 GCCACATGTACCAAAAAGTGACACATAGCACGCCACATGTACCAAAAAG

       6839 TGATACGTGG


Statistics
Matches: 43,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  53   43  1.00

ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16


Consensus pattern (53 bp):   
GCCACATGTACCAAAAAGTGACACATAGCACGCCACATGTACCAAAAAGCCGT

Found at i:6856 original size:31 final size:31

Alignment explanation


    Indices: 6787--6860  Score: 94
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       6777 ACTAAAAAGC

                                          *
       6787 CGTGCCACATGTACCAAAAAGTGACACATAT
          1 CGTGCCACATGTACCAAAAAGTGACACATAG

             **                     *  * * 
       6818 CACGCCACATGTACCAAAAAGTGATACGTGG
          1 CGTGCCACATGTACCAAAAAGTGACACATAG

                        
       6849 CGTGCCACATGT
          1 CGTGCCACATGT

       6861 TTCAAAAAAT


Statistics
Matches: 35,  Mismatches: 8, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  31   35  1.00

ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19


Consensus pattern (31 bp):   
CGTGCCACATGTACCAAAAAGTGACACATAG
Done.