Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011664.1 Corchorus capsularis cultivar CVL-1 contig11685, 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: 27758
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:2531 original size:2 final size:2

Alignment explanation


    Indices: 2524--2562  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       2514 TTCTTACTTT

                                                         *            
       2524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2563 TTAAATTGGG


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:6135 original size:19 final size:18

Alignment explanation


    Indices: 6102--6137  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6092 TTGAAATAAT

                              
       6102 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       6120 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       6138 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:14923 original size:30 final size:30

Alignment explanation


    Indices: 14897--14956  Score: 84
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      14887 GGATCGCATG

                *      *   *   *          
      14897 TGACTGGCCATTGCATGGAGCAATCGCACA
          1 TGACCGGCCATGGCAAGGACCAATCGCACA

                                          
      14927 TGACCGGCCATGGCAAGGACCAATCGCACA
          1 TGACCGGCCATGGCAAGGACCAATCGCACA

      14957 AGGCCGGGCA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15


Consensus pattern (30 bp):   
TGACCGGCCATGGCAAGGACCAATCGCACA

Found at i:25184 original size:27 final size:27

Alignment explanation


    Indices: 25149--25202  Score: 108
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      25139 TGTTGGATTT

                                       
      25149 AAATTCTAAATTACCTTAATTAGATAA
          1 AAATTCTAAATTACCTTAATTAGATAA

                                       
      25176 AAATTCTAAATTACCTTAATTAGATAA
          1 AAATTCTAAATTACCTTAATTAGATAA

      25203 GATTACCGAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37


Consensus pattern (27 bp):   
AAATTCTAAATTACCTTAATTAGATAA
Done.