Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022103.1 Corchorus olitorius cultivar O-4 contig22136, 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: 9308
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:16 original size:5 final size:5

Alignment explanation


    Indices: 2--40  Score: 53
    Period size: 5  Copynumber: 7.8  Consensus size: 5

          1 A

                                         *                 
          2 TTTTC TTTTTC TTTTC TTTTC TTTTT TTTTC TTTT- TTTT
          1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT

         41 TTAAACTTGG


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   4    4  0.13
   5   22  0.71
   6    5  0.16

ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87


Consensus pattern (5 bp):   
TTTTC

Found at i:42 original size:11 final size:10

Alignment explanation


    Indices: 2--41  Score: 62
    Period size: 10  Copynumber: 3.9  Consensus size: 10

          1 A

                       
          2 TTTTCTTTTTC
          1 TTTT-TTTTTC

                *     
         13 TTTTCTTTTC
          1 TTTTTTTTTC

                      
         23 TTTTTTTTTC
          1 TTTTTTTTTC

                     
         33 TTTTTTTTT
          1 TTTTTTTTT

         42 TAAACTTGGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  10   23  0.85
  11    4  0.15

ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88


Consensus pattern (10 bp):   
TTTTTTTTTC

Found at i:111 original size:25 final size:25

Alignment explanation


    Indices: 82--139  Score: 71
    Period size: 25  Copynumber: 2.3  Consensus size: 25

         72 CTGGGCCATA

                                     
         82 CGCTGGCCCGCGCACCAGGCCAGGG
          1 CGCTGGCCCGCGCACCAGGCCAGGG

                  *   *  *       *   
        107 CGCTGGGCCGTGCGCCAGGCCTGGG
          1 CGCTGGCCCGCGCACCAGGCCAGGG

                    
        132 CGCCTGGC
          1 CG-CTGGC

        140 TGGTCCAAGT


Statistics
Matches: 27,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  25   23  0.85
  26    4  0.15

ACGTcount: A:0.07, C:0.41, G:0.43, T:0.09


Consensus pattern (25 bp):   
CGCTGGCCCGCGCACCAGGCCAGGG
Done.