Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014435.1 Corchorus olitorius cultivar O-4 contig14468, 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: 2068
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29


Found at i:1475 original size:20 final size:19

Alignment explanation


    Indices: 1450--1493  Score: 61
    Period size: 20  Copynumber: 2.3  Consensus size: 19

       1440 CCCAATAATA

                                
       1450 AAAAATAAAAAAGAAGAAAG
          1 AAAAATAAAAAAGAA-AAAG

                  *          * 
       1470 AAAAATGAAAAAGAAAATG
          1 AAAAATAAAAAAGAAAAAG

                 
       1489 AAAAA
          1 AAAAA

       1494 AAACACTTGG


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19    8  0.36
  20   14  0.64

ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07


Consensus pattern (19 bp):   
AAAAATAAAAAAGAAAAAG

Found at i:1494 original size:13 final size:13

Alignment explanation


    Indices: 1450--1493  Score: 54
    Period size: 12  Copynumber: 3.4  Consensus size: 13

       1440 CCCAATAATA

                 *     * 
       1450 AAAAATAAAAAAG
          1 AAAAAGAAAAATG

                          
       1463 AAGAAAGAAAAATG
          1 AA-AAAGAAAAATG

                         
       1477 AAAAAG-AAAATG
          1 AAAAAGAAAAATG

                 
       1489 AAAAA
          1 AAAAA

       1494 AAACACTTGG


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  12   11  0.39
  13    6  0.21
  14   11  0.39

ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07


Consensus pattern (13 bp):   
AAAAAGAAAAATG

Found at i:1884 original size:16 final size:16

Alignment explanation


    Indices: 1860--1908  Score: 80
    Period size: 16  Copynumber: 3.0  Consensus size: 16

       1850 CCACTCCATC

                            
       1860 AAGAAATTCAAAAAAA
          1 AAGAAATTCAAAAAAA

                *           
       1876 AAGATATTCAAAAAAA
          1 AAGAAATTCAAAAAAA

                             
       1892 AGAGAAATTCAAAAAAA
          1 A-AGAAATTCAAAAAAA

       1909 TCAAATCAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  16   16  0.53
  17   14  0.47

ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14


Consensus pattern (16 bp):   
AAGAAATTCAAAAAAA

Found at i:1891 original size:17 final size:17

Alignment explanation


    Indices: 1860--1908  Score: 73
    Period size: 17  Copynumber: 2.9  Consensus size: 17

       1850 CCACTCCATC

                             
       1860 AAGAAATTC-AAAAAAA
          1 AAGAAATTCAAAAAAAA

                *            
       1876 AAGATATTCAAAAAAAA
          1 AAGAAATTCAAAAAAAA

            *               
       1893 GAGAAATTCAAAAAAA
          1 AAGAAATTCAAAAAAA

       1909 TCAAATCAAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  16    8  0.28
  17   21  0.72

ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14


Consensus pattern (17 bp):   
AAGAAATTCAAAAAAAA
Done.