Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000523.1 Corchorus capsularis cultivar CVL-1 contig00523, 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: 1961
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:1562 original size:16 final size:18

Alignment explanation


    Indices: 1541--1573  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1531 TTAGGGGAAA

                              
       1541 GTGAT-GAA-CTGTGGAG
          1 GTGATGGAAGCTGTGGAG

                             
       1557 GTGATGGAAGCTGTGGA
          1 GTGATGGAAGCTGTGGA

       1574 ACTTGCATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    5  0.33
  17    3  0.20
  18    7  0.47

ACGTcount: A:0.24, C:0.06, G:0.45, T:0.24


Consensus pattern (18 bp):   
GTGATGGAAGCTGTGGAG

Found at i:1772 original size:16 final size:16

Alignment explanation


    Indices: 1705--1774  Score: 54
    Period size: 16  Copynumber: 4.4  Consensus size: 16

       1695 AAAAGTCAAC

                         *  
       1705 AACCCGA-ACCCGTCT
          1 AACCCGAGACCCGACT

            *      *   *    
       1720 GACCCGAAACCTGACT
          1 AACCCGAGACCCGACT

                  *       * 
       1736 AACCCGTGACCCGATT
          1 AACCCGAGACCCGACT

            *                
       1752 GACCCGAGACCCGTA-T
          1 AACCCGAGACCCG-ACT

                   
       1768 AACCCGA
          1 AACCCGA

       1775 AATCCATATG


Statistics
Matches: 42,  Mismatches: 11, Indels: 3
        0.75            0.20        0.05

Matches are distributed among these distances:
  15    6  0.14
  16   35  0.83
  17    1  0.02

ACGTcount: A:0.29, C:0.40, G:0.19, T:0.13


Consensus pattern (16 bp):   
AACCCGAGACCCGACT

Found at i:1823 original size:16 final size:16

Alignment explanation


    Indices: 1784--1828  Score: 63
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       1774 AAATCCATAT

                     *      
       1784 GACCCGAAATCCGTGA
          1 GACCCGAAACCCGTGA

            *  *            
       1800 AACGCGAAACCCGTGA
          1 GACCCGAAACCCGTGA

                         
       1816 GACCCGAAACCCG
          1 GACCCGAAACCCG

       1829 AAAAGTTGAC


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.33, C:0.36, G:0.24, T:0.07


Consensus pattern (16 bp):   
GACCCGAAACCCGTGA
Done.