Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001287.1 Corchorus capsularis cultivar CVL-1 contig01287, 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: 2561
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:1245 original size:16 final size:15

Alignment explanation


    Indices: 1223--1351  Score: 95
    Period size: 16  Copynumber: 8.5  Consensus size: 15

       1213 AACAATTTTC

                           
       1223 TCGGGTCATTCGGGT
          1 TCGGGTCATTCGGGT

                       *    
       1238 TACGGGTCATTTGGGT
          1 T-CGGGTCATTCGGGT

                  *    *   
       1254 TCGGGTTATT-TGG-
          1 TCGGGTCATTCGGGT

                           
       1267 --GGGTCATTCGGGT
          1 TCGGGTCATTCGGGT

                      *      
       1280 CTCGGGTCATACGGGTT
          1 -TCGGGTCATTCGGG-T

                  *    **  
       1297 TCGGGTAATTCTAGT
          1 TCGGGTCATTCGGGT

                *            
       1312 CTCGAGTCATTCGGGTT
          1 -TCGGGTCATTCGGG-T

             *             
       1329 TTGGGTCATTCGGGT
          1 TCGGGTCATTCGGGT

                    
       1344 CTCGGGTC
          1 -TCGGGTC

       1352 TACCGGGTCT


Statistics
Matches: 87,  Mismatches: 17, Indels: 19
        0.71            0.14        0.15

Matches are distributed among these distances:
  11    7  0.08
  12    2  0.02
  14    2  0.02
  15   11  0.13
  16   63  0.72
  17    2  0.02

ACGTcount: A:0.10, C:0.18, G:0.36, T:0.36


Consensus pattern (15 bp):   
TCGGGTCATTCGGGT

Found at i:1315 original size:32 final size:32

Alignment explanation


    Indices: 1267--1366  Score: 103
    Period size: 32  Copynumber: 3.1  Consensus size: 32

       1257 GGTTATTTGG

                *     *                     
       1267 GGGTCATTCGGGTCTCGGGTCATACGGGTTTC
          1 GGGTAATTCGAGTCTCGGGTCATACGGGTTTC

                     *       *     *       *
       1299 GGGTAATTCTAGTCTCGAGTCATTCGGGTTTT
          1 GGGTAATTCGAGTCTCGGGTCATACGGGTTTC

                *     *                   *  
       1331 GGGTCATTCGGGTCTCGGGTC-TACCGGGTCTC
          1 GGGTAATTCGAGTCTCGGGTCATA-CGGGTTTC

                
       1363 GGGT
          1 GGGT

       1367 TGGGCGGGTT


Statistics
Matches: 54,  Mismatches: 13, Indels: 2
        0.78            0.19        0.03

Matches are distributed among these distances:
  31    1  0.02
  32   53  0.98

ACGTcount: A:0.10, C:0.21, G:0.36, T:0.33


Consensus pattern (32 bp):   
GGGTAATTCGAGTCTCGGGTCATACGGGTTTC

Found at i:1957 original size:18 final size:19

Alignment explanation


    Indices: 1931--1972  Score: 59
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       1921 CAAACAGGGA

                *         *    
       1931 AGAGGCTCTCA-TGTAGAG
          1 AGAGACTCTCATTGAAGAG

                               
       1949 AGAGACTCTCATTGAAGAG
          1 AGAGACTCTCATTGAAGAG

                 
       1968 AGAGA
          1 AGAGA

       1973 GAGTTATTAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18   10  0.48
  19   11  0.52

ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19


Consensus pattern (19 bp):   
AGAGACTCTCATTGAAGAG

Done.