Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017523.1 Corchorus olitorius cultivar O-4 contig17556, 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: 14274
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29


Found at i:1305 original size:31 final size:31

Alignment explanation


    Indices: 1268--1397  Score: 197
    Period size: 31  Copynumber: 4.2  Consensus size: 31

       1258 ATGAGGCATT

                                           
       1268 CCACGTGTCACTTTTTGGTACACGTGGCGTG
          1 CCACGTGTCACTTTTTGGTACACGTGGCGTG

                                  *        
       1299 CCACGTGTCACTTTTTGGTACATGTGGCGTG
          1 CCACGTGTCACTTTTTGGTACACGTGGCGTG

                *    *             *       
       1330 CCACATGTCGCTTTTTGGTACACATGGCGTG
          1 CCACGTGTCACTTTTTGGTACACGTGGCGTG

                *    *                  *  
       1361 CCACATGTCGCTTTTTGGTACACGTGGCATG
          1 CCACGTGTCACTTTTTGGTACACGTGGCGTG

                  
       1392 CCACGT
          1 CCACGT

       1398 CGGACACCGT


Statistics
Matches: 91,  Mismatches: 8, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  31   91  1.00

ACGTcount: A:0.15, C:0.26, G:0.27, T:0.32


Consensus pattern (31 bp):   
CCACGTGTCACTTTTTGGTACACGTGGCGTG

Found at i:1347 original size:62 final size:61

Alignment explanation


    Indices: 1235--1395  Score: 207
    Period size: 62  Copynumber: 2.6  Consensus size: 61

       1225 AAAAATGACA

                *                 *    *     *    *                  *   
       1235 CGTGGCACGTGTCCTTTTT-GTGCATGAGGCATTCCACGTGTCACTTTTTGGTACACGTGG
          1 CGTGCCACGTGTCCTTTTTGGTACATGTGGCATGCCACATGTCACTTTTTGGTACACATGG

                                            *           *                 
       1295 CGTGCCACGTGTCACTTTTTGGTACATGTGGCGTGCCACATGTCGCTTTTTGGTACACATGG
          1 CGTGCCACGTGTC-CTTTTTGGTACATGTGGCATGCCACATGTCACTTTTTGGTACACATGG

                    *                 *            
       1357 CGTGCCACATGTCGCTTTTTGGTACACGTGGCATGCCAC
          1 CGTGCCACGTGTC-CTTTTTGGTACATGTGGCATGCCAC

       1396 GTCGGACACC


Statistics
Matches: 87,  Mismatches: 12, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  60   12  0.14
  61    6  0.07
  62   69  0.79

ACGTcount: A:0.14, C:0.25, G:0.27, T:0.33


Consensus pattern (61 bp):   
CGTGCCACGTGTCCTTTTTGGTACATGTGGCATGCCACATGTCACTTTTTGGTACACATGG

Found at i:4601 original size:31 final size:31

Alignment explanation


    Indices: 4555--4639  Score: 127
    Period size: 31  Copynumber: 2.8  Consensus size: 31

       4545 TCCACTTTGC

                  *                  *     
       4555 AAAATTAC-CAATTTGAGTCTAAACTTTTCA
          1 AAAATTGCTCAATTTGAGTCTAAACATTTCA

               *                           
       4585 AAAGTTGCTCAATTTGAGTCTAAACATTTCA
          1 AAAATTGCTCAATTTGAGTCTAAACATTTCA

                              *     
       4616 AAAATTGCTCAATTTGAGACTAAA
          1 AAAATTGCTCAATTTGAGTCTAAA

       4640 AACATAAAAA


Statistics
Matches: 49,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  30    6  0.12
  31   43  0.88

ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34


Consensus pattern (31 bp):   
AAAATTGCTCAATTTGAGTCTAAACATTTCA
Done.