Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000284.1 Corchorus olitorius cultivar O-4 contig00284, 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: 2060
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28


Found at i:1798 original size:26 final size:27

Alignment explanation


    Indices: 1748--1798  Score: 70
    Period size: 26  Copynumber: 1.9  Consensus size: 27

       1738 GCAACACAAG

                                *      
       1748 AAAATCGTTAAAACCAATATCATAATC
          1 AAAATCGTTAAAACCAATATAATAATC

                                      
       1775 AAAATCG-TAAAACCAA-AGTAATAA
          1 AAAATCGTTAAAACCAATA-TAATAA

       1799 ACCAAATCAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  25    1  0.05
  26   14  0.64
  27    7  0.32

ACGTcount: A:0.57, C:0.16, G:0.06, T:0.22


Consensus pattern (27 bp):   
AAAATCGTTAAAACCAATATAATAATC

Found at i:1804 original size:27 final size:27

Alignment explanation


    Indices: 1748--1804  Score: 64
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       1738 GCAACACAAG

                                *    * 
       1748 AAAATCGTTAAAACCAATATCATAATC
          1 AAAATCGTTAAAACCAATATAATAACC

                                         
       1775 AAAATCG-TAAAACCAA-AGTAATAAACC
          1 AAAATCGTTAAAACCAATA-TAAT-AACC

               
       1802 AAA
          1 AAA

       1805 TCAGTCAAAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  25    1  0.04
  26   12  0.46
  27   13  0.50

ACGTcount: A:0.58, C:0.18, G:0.05, T:0.19


Consensus pattern (27 bp):   
AAAATCGTTAAAACCAATATAATAACC

Found at i:1805 original size:26 final size:27

Alignment explanation


    Indices: 1748--1806  Score: 68
    Period size: 26  Copynumber: 2.2  Consensus size: 27

       1738 GCAACACAAG

                                *    * 
       1748 AAAATCGTTAAAACCAATATCATAATC
          1 AAAATCGTTAAAACCAATATAATAAAC

                                        
       1775 AAAATCG-TAAAACCAA-AGTAATAAAC
          1 AAAATCGTTAAAACCAATA-TAATAAAC

            *     
       1801 CAAATC
          1 AAAATC

       1807 AGTCAAATAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  25    1  0.04
  26   20  0.71
  27    7  0.25

ACGTcount: A:0.56, C:0.19, G:0.05, T:0.20


Consensus pattern (27 bp):   
AAAATCGTTAAAACCAATATAATAAAC
Done.