Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013317.1 Corchorus capsularis cultivar CVL-1 contig13338, 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: 9210
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:2251 original size:49 final size:49

Alignment explanation


    Indices: 2126--2267  Score: 196
    Period size: 49  Copynumber: 2.9  Consensus size: 49

       2116 AAACACCGAG

                        *                     *  *    *     *
       2126 CTTTCCCAAGCTCA-AACAAGTGCTCCCCGCACTTATCACAAACCTAAG
          1 CTTTCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAATCCTAAA

                       *                                      
       2174 CTTTCCCCAAGTTTAGAACAAGTGCTCCCCGCACTGATTACAATCCTAAA
          1 CTTT-CCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAATCCTAAA

                                         *     *        
       2224 CTTTCCCAAGCTTAGAACAAGTGCTCCCCACACTGTTTACAATC
          1 CTTTCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAATC

       2268 AAAGATATAG


Statistics
Matches: 83,  Mismatches: 9, Indels: 3
        0.87            0.09        0.03

Matches are distributed among these distances:
  48    4  0.05
  49   45  0.54
  50   34  0.41

ACGTcount: A:0.30, C:0.35, G:0.11, T:0.25


Consensus pattern (49 bp):   
CTTTCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAATCCTAAA

Found at i:6039 original size:33 final size:33

Alignment explanation


    Indices: 5995--6059  Score: 103
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       5985 ATTTAGATAT

                                             
       5995 ATGTGCACTGTAAAACGAAAAGAAAATGAGATC
          1 ATGTGCACTGTAAAACGAAAAGAAAATGAGATC

                  *        * *              
       6028 ATGTGCCCTGTAAAATGGAAAGAAAATGAGAT
          1 ATGTGCACTGTAAAACGAAAAGAAAATGAGAT

       6060 AGCCCGAATA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  33   29  1.00

ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20


Consensus pattern (33 bp):   
ATGTGCACTGTAAAACGAAAAGAAAATGAGATC
Done.