Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009900.1 Corchorus olitorius cultivar O-4 contig09932, 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: 4061
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:913 original size:18 final size:17

Alignment explanation


    Indices: 890--927  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

        880 CCCAAATTAC

                              
        890 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
        908 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
        925 TTA
          1 TTA

        928 AATGAATTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    8  0.40
  18   12  0.60

ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32


Consensus pattern (17 bp):   
TTATGGAAATTAGGAAA

Found at i:925 original size:8 final size:9

Alignment explanation


    Indices: 894--927  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

        884 AATTACTTAT

                     
        894 GGAAATTAG
          1 GGAAATTAG

                    *
        903 GGAAATTAT
          1 GGAAATTAG

                     
        912 GGAAATTA-
          1 GGAAATTAG

                    
        920 GGAAATTA
          1 GGAAATTA

        928 AATGAATTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   8    8  0.33
   9   16  0.67

ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26


Consensus pattern (9 bp):   
GGAAATTAG

Found at i:3056 original size:32 final size:33

Alignment explanation


    Indices: 2988--3061  Score: 96
    Period size: 32  Copynumber: 2.3  Consensus size: 33

       2978 CCGCCCTAGG

                 *              *   ***      
       2988 AGGGCAGCATGCCATGGTTGGTGCTGGCCTCCT
          1 AGGGCGGCATGCCATGGTTGATGCCACCCTCCT

                                             
       3021 AGGGCGGCATGCCATGGTT-ATGCCACCCTCCT
          1 AGGGCGGCATGCCATGGTTGATGCCACCCTCCT

                     
       3053 AGGGCGGCA
          1 AGGGCGGCA

       3062 CCGTAAATTT


Statistics
Matches: 36,  Mismatches: 5, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  32   18  0.50
  33   18  0.50

ACGTcount: A:0.15, C:0.30, G:0.35, T:0.20


Consensus pattern (33 bp):   
AGGGCGGCATGCCATGGTTGATGCCACCCTCCT
Done.