Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009372.1 Corchorus capsularis cultivar CVL-1 contig09393, 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: 14747
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1705 original size:105 final size:105

Alignment explanation


    Indices: 1557--1746  Score: 317
    Period size: 105  Copynumber: 1.8  Consensus size: 105

       1547 GAAGGAACAA

                                                                   *    *  * 
       1557 CTTGGAGGTTGCTCCCGACTTCAGAGATAGCACTATGGCAGCAAAGGGAAAGAATTTCCGTTGTA
          1 CTTGGAGGTTGCTCCCGACTTCAGAGATAGCACTATGGCAGCAAAGGGAAAGAATCTCCGCTGCA

            *         *                             
       1622 GTGTTGACTTGCTGCAGCTGCTTTTAGAAGGAACAACTTG
         66 ATGTTGACTTACTGCAGCTGCTTTTAGAAGGAACAACTTG

                              *                 *                            
       1662 CTTGGAGGTTGCTCCCGATTTCAGAGATAGCACTATTGCAGCAAAGGGAAAGAATCTCCGCTGCA
          1 CTTGGAGGTTGCTCCCGACTTCAGAGATAGCACTATGGCAGCAAAGGGAAAGAATCTCCGCTGCA

                                
       1727 ATGTTGACTTACTGCAGCTG
         66 ATGTTGACTTACTGCAGCTG

       1747 TCGAGAATCT


Statistics
Matches: 78,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 105   78  1.00

ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27


Consensus pattern (105 bp):   
CTTGGAGGTTGCTCCCGACTTCAGAGATAGCACTATGGCAGCAAAGGGAAAGAATCTCCGCTGCA
ATGTTGACTTACTGCAGCTGCTTTTAGAAGGAACAACTTG

Found at i:2769 original size:2 final size:2

Alignment explanation


    Indices: 2762--2792  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2752 AAACGAAAGG

                                                          
       2762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2793 TAAACAGAGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.