Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016393.1 Corchorus capsularis cultivar CVL-1 contig16414, 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: 2756
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:2128 original size:5 final size:5

Alignment explanation


    Indices: 2115--2147  Score: 50
    Period size: 5  Copynumber: 6.8  Consensus size: 5

       2105 GGTTCAAGGG

                      *                             
       2115 GGGGT GGGGA GGGGT GGGGT GGGGT GGGG- GGGG
          1 GGGGT GGGGT GGGGT GGGGT GGGGT GGGGT GGGG

       2148 AGTAGGGAGG


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   4    4  0.15
   5   22  0.85

ACGTcount: A:0.03, C:0.00, G:0.85, T:0.12


Consensus pattern (5 bp):   
GGGGT

Found at i:2130 original size:10 final size:10

Alignment explanation


    Indices: 2115--2159  Score: 54
    Period size: 10  Copynumber: 4.4  Consensus size: 10

       2105 GGTTCAAGGG

                      
       2115 GGGGTGGGGA
          1 GGGGTGGGGA

                     *
       2125 GGGGTGGGGT
          1 GGGGTGGGGA

                     *
       2135 GGGGTGGGGG
          1 GGGGTGGGGA

                  *    
       2145 GGGAGTAGGGA
          1 GGG-GTGGGGA

                
       2156 GGGG
          1 GGGG

       2160 GAGGAGGATG


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  10   22  0.73
  11    8  0.27

ACGTcount: A:0.09, C:0.00, G:0.80, T:0.11


Consensus pattern (10 bp):   
GGGGTGGGGA

Found at i:2135 original size:15 final size:15

Alignment explanation


    Indices: 2112--2160  Score: 62
    Period size: 15  Copynumber: 3.2  Consensus size: 15

       2102 TTTGGTTCAA

                           
       2112 GGGGGGGTGGGGAGG
          1 GGGGGGGTGGGGAGG

              *         *  
       2127 GGTGGGGTGGGGTGG
          1 GGGGGGGTGGGGAGG

                     *      
       2142 GGGGGGAGTAGGGAGG
          1 GGGGGG-GTGGGGAGG

               
       2158 GGG
          1 GGG

       2161 AGGAGGATGG


Statistics
Matches: 28,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  15   18  0.64
  16   10  0.36

ACGTcount: A:0.08, C:0.00, G:0.82, T:0.10


Consensus pattern (15 bp):   
GGGGGGGTGGGGAGG

Found at i:2304 original size:27 final size:27

Alignment explanation


    Indices: 2274--2344  Score: 115
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       2264 ATTAGGGTCG

                                       
       2274 CCCAGGGGCATTTTGGTCATTTTTGCA
          1 CCCAGGGGCATTTTGGTCATTTTTGCA

                    *                  
       2301 CCCAGGGGTATTTTGGTCATTTTTGCA
          1 CCCAGGGGCATTTTGGTCATTTTTGCA

            *   *            
       2328 TCCAAGGGCATTTTGGT
          1 CCCAGGGGCATTTTGGT

       2345 AACTTGGTGA


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   40  1.00

ACGTcount: A:0.15, C:0.20, G:0.27, T:0.38


Consensus pattern (27 bp):   
CCCAGGGGCATTTTGGTCATTTTTGCA
Done.