Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015080.1 Corchorus capsularis cultivar CVL-1 contig15101, 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: 3007
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30


Found at i:112 original size:16 final size:16

Alignment explanation


    Indices: 85--159  Score: 98
    Period size: 16  Copynumber: 4.8  Consensus size: 16

         75 GTCGGGTTGA

                *           
         85 TCGGATTCGGGTCATT
          1 TCGGGTTCGGGTCATT

                   *        
        101 TCGGGTTTGGGTCATT
          1 TCGGGTTCGGGTCATT

                         *  
        117 TCGGGTTCGGGTCGTT
          1 TCGGGTTCGGGTCATT

                *           
        133 T-GGATTCGGGTCATT
          1 TCGGGTTCGGGTCATT

             *          
        148 TTGGGTTCGGGT
          1 TCGGGTTCGGGT

        160 ACCCAAAAAT


Statistics
Matches: 51,  Mismatches: 7, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  15   13  0.25
  16   38  0.75

ACGTcount: A:0.07, C:0.15, G:0.39, T:0.40


Consensus pattern (16 bp):   
TCGGGTTCGGGTCATT

Found at i:147 original size:31 final size:32

Alignment explanation


    Indices: 85--159  Score: 98
    Period size: 31  Copynumber: 2.4  Consensus size: 32

         75 GTCGGGTTGA

                *               *  *        
         85 TCGGATTCGGGTCATTTCGGGTTTGGGTCATT
          1 TCGGGTTCGGGTCATTTCGGATTCGGGTCATT

                         *                  
        117 TCGGGTTCGGGTCGTTT-GGATTCGGGTCATT
          1 TCGGGTTCGGGTCATTTCGGATTCGGGTCATT

             *          
        148 TTGGGTTCGGGT
          1 TCGGGTTCGGGT

        160 ACCCAAAAAT


Statistics
Matches: 38,  Mismatches: 5, Indels: 1
        0.86            0.11        0.02

Matches are distributed among these distances:
  31   23  0.61
  32   15  0.39

ACGTcount: A:0.07, C:0.15, G:0.39, T:0.40


Consensus pattern (32 bp):   
TCGGGTTCGGGTCATTTCGGATTCGGGTCATT

Found at i:1519 original size:46 final size:46

Alignment explanation


    Indices: 1466--1557  Score: 157
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       1456 TTTTCCTTGA

                                               *          
       1466 ATATTTCCTTCTTACCATAAATCCCATGATTGACGTCTTAAATCAG
          1 ATATTTCCTTCTTACCATAAATCCCATGATTGACGCCTTAAATCAG

                                *  *                      
       1512 ATATTTCCTTCTTACCATAATTCTCATGATTGACGCCTTAAATCAG
          1 ATATTTCCTTCTTACCATAAATCCCATGATTGACGCCTTAAATCAG

       1558 TTTCACCGTA


Statistics
Matches: 43,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  46   43  1.00

ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38


Consensus pattern (46 bp):   
ATATTTCCTTCTTACCATAAATCCCATGATTGACGCCTTAAATCAG
Done.