Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023942.1 Corchorus olitorius cultivar O-4 contig23975, 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: 23268
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:8917 original size:21 final size:21

Alignment explanation


    Indices: 8893--8936  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       8883 TCTTGCTCTT

                *      *   *     
       8893 TTCATTGGATCTAATGGCATC
          1 TTCAATGGATCAAATAGCATC

                                 
       8914 TTCAATGGATCAAATAGCATC
          1 TTCAATGGATCAAATAGCATC

              
       8935 TT
          1 TT

       8937 TGGCATCTCC


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36


Consensus pattern (21 bp):   
TTCAATGGATCAAATAGCATC

Found at i:17895 original size:41 final size:37

Alignment explanation


    Indices: 17810--17921  Score: 152
    Period size: 41  Copynumber: 2.9  Consensus size: 37

      17800 ATTTAGAAGT

                   *                             
      17810 TTTTCAAATAGGGAAAGATCCCATCAAGTTTTCAAAG
          1 TTTTCAATTAGGGAAAGATCCCATCAAGTTTTCAAAG

                                      *              
      17847 TTTTCAATTTAGGGAAAGATCCCATCCAGTCTTTTTCAAAG
          1 TTTTCAA-TTAGGGAAAGATCCCATCAAG---TTTTCAAAG

                                              
      17888 TTTTCAATTAGGGGAAAGATCCCATCAAAGTTTT
          1 TTTTCAATTA-GGGAAAGATCCCATC-AAGTTTT

      17922 TAAAATTGAG


Statistics
Matches: 66,  Mismatches: 3, Indels: 10
        0.84            0.04        0.13

Matches are distributed among these distances:
  37    7  0.11
  38   19  0.29
  39    4  0.06
  40    3  0.05
  41   31  0.47
  42    2  0.03

ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Consensus pattern (37 bp):   
TTTTCAATTAGGGAAAGATCCCATCAAGTTTTCAAAG

Found at i:22088 original size:16 final size:16

Alignment explanation


    Indices: 22067--22104  Score: 67
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      22057 CAAATTGCAA

                        *   
      22067 GGAGAGTTGATCTAAT
          1 GGAGAGTTGATCCAAT

                            
      22083 GGAGAGTTGATCCAAT
          1 GGAGAGTTGATCCAAT

                  
      22099 GGAGAG
          1 GGAGAG

      22105 ATTAAGGCAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.32, C:0.08, G:0.37, T:0.24


Consensus pattern (16 bp):   
GGAGAGTTGATCCAAT
Done.