Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022254.1 Corchorus olitorius cultivar O-4 contig22287, 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: 5898
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29


Found at i:1890 original size:29 final size:30

Alignment explanation


    Indices: 1858--1914  Score: 82
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       1848 CTAGGATTTA

                                           
       1858 GACATTTTGCTCC-CTAAACTT-TAATTTTG
          1 GACATTTTGC-CCACTAAACTTATAATTTTG

                         *              
       1887 GACATTTTGCCCATTAAACTTATAATTT
          1 GACATTTTGCCCACTAAACTTATAATTT

       1915 GGAGTCATTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  28    2  0.08
  29   17  0.68
  30    6  0.24

ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44


Consensus pattern (30 bp):   
GACATTTTGCCCACTAAACTTATAATTTTG

Found at i:1915 original size:29 final size:28

Alignment explanation


    Indices: 1853--1917  Score: 78
    Period size: 29  Copynumber: 2.2  Consensus size: 28

       1843 GACTTCTAGG

                *                       
       1853 ATTTAGACATTTTGCTCCCTAAACTTTA
          1 ATTTGGACATTTTGCTCCCTAAACTTTA

                                *          
       1881 ATTTTGGACATTTTGC-CCATTAAACTTATA
          1 A-TTTGGACATTTTGCTCC-CTAAACTT-TA

                   
       1911 ATTTGGA
          1 ATTTGGA

       1918 GTCATTTTAG


Statistics
Matches: 32,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  28    3  0.09
  29   26  0.81
  30    3  0.09

ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43


Consensus pattern (28 bp):   
ATTTGGACATTTTGCTCCCTAAACTTTA

Found at i:2510 original size:26 final size:26

Alignment explanation


    Indices: 2476--2527  Score: 104
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       2466 GGTAGTAACA

                                      
       2476 AACCCAATATAGTATTAGACATAAAC
          1 AACCCAATATAGTATTAGACATAAAC

                                      
       2502 AACCCAATATAGTATTAGACATAAAC
          1 AACCCAATATAGTATTAGACATAAAC

       2528 CCGGCCGCAG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23


Consensus pattern (26 bp):   
AACCCAATATAGTATTAGACATAAAC
Done.