Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014462.1 Corchorus capsularis cultivar CVL-1 contig14483, 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: 14340
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:7648 original size:19 final size:18

Alignment explanation


    Indices: 7613--7648  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7603 AAATATAAAT

                              
       7613 CAAAACCACCAAAACCGC
          1 CAAAACCACCAAAACCGC

                       *      
       7631 CAAAACCGACCGAAACCG
          1 CAAAACC-ACCAAAACCG

       7649 ACCGCCACCG


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:0.47, C:0.42, G:0.11, T:0.00


Consensus pattern (18 bp):   
CAAAACCACCAAAACCGC

Found at i:7652 original size:10 final size:10

Alignment explanation


    Indices: 7613--7651  Score: 55
    Period size: 9  Copynumber: 4.1  Consensus size: 10

       7603 AAATATAAAT

                      
       7613 CAAAACC-AC
          1 CAAAACCGAC

                      
       7622 CAAAACCG-C
          1 CAAAACCGAC

                      
       7631 CAAAACCGAC
          1 CAAAACCGAC

             *        
       7641 CGAAACCGAC
          1 CAAAACCGAC

             
       7651 C
          1 C

       7652 GCCACCGACA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
   9   16  0.59
  10   11  0.41

ACGTcount: A:0.46, C:0.44, G:0.10, T:0.00


Consensus pattern (10 bp):   
CAAAACCGAC

Found at i:8198 original size:27 final size:26

Alignment explanation


    Indices: 8142--8217  Score: 98
    Period size: 26  Copynumber: 2.8  Consensus size: 26

       8132 GAAAAACCCC

                       *         *   *
       8142 CACTTTCAAATCACTTTTTTTTAGAG
          1 CACTTTCAAATTACTTTTTTTAAGAA

                                       
       8168 CACTTTCAAATTACTTTTTTCTAAGAA
          1 CACTTTCAAATTACTTTTTT-TAAGAA

                                   
       8195 CACTTTCAAATTATACTTTTTTT
          1 CACTTTCAAA-T-TACTTTTTTT

       8218 CAAATTACTG


Statistics
Matches: 44,  Mismatches: 3, Indels: 4
        0.86            0.06        0.08

Matches are distributed among these distances:
  26   19  0.43
  27   14  0.32
  28    2  0.05
  29    9  0.20

ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49


Consensus pattern (26 bp):   
CACTTTCAAATTACTTTTTTTAAGAA

Found at i:14094 original size:54 final size:54

Alignment explanation


    Indices: 14030--14137  Score: 207
    Period size: 54  Copynumber: 2.0  Consensus size: 54

      14020 ATCGATTCTC

                                                                  
      14030 GACATTGCGTTTCCGAGGATTAGTCAGATATGTGAATTCAGACAGTCCAATGGG
          1 GACATTGCGTTTCCGAGGATTAGTCAGATATGTGAATTCAGACAGTCCAATGGG

                         *                                        
      14084 GACATTGCGTTTCTGAGGATTAGTCAGATATGTGAATTCAGACAGTCCAATGGG
          1 GACATTGCGTTTCCGAGGATTAGTCAGATATGTGAATTCAGACAGTCCAATGGG

      14138 TTGGCAAATG


Statistics
Matches: 53,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  54   53  1.00

ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29


Consensus pattern (54 bp):   
GACATTGCGTTTCCGAGGATTAGTCAGATATGTGAATTCAGACAGTCCAATGGG
Done.