Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001305.1 Corchorus olitorius cultivar O-4 contig01305, 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, 600

Length: 1001
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39


Found at i:671 original size:38 final size:38

Alignment explanation


    Indices: 575--722  Score: 226
    Period size: 38  Copynumber: 3.9  Consensus size: 38

        565 GGCTGTGCAT

                    *                     *        
        575 AGTGGACCTGTACCTCAGGGGGTTAAACTGATGGTAAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG

                     *    *                       
        614 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG

                       *                          
        652 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG

                       *                      
        690 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG

        723 CTAGACTCGA


Statistics
Matches: 102,  Mismatches: 7, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  37    9  0.09
  38   62  0.61
  39   31  0.30

ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23


Consensus pattern (38 bp):   
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG

Found at i:763 original size:6 final size:6

Alignment explanation


    Indices: 752--788  Score: 67
    Period size: 6  Copynumber: 6.3  Consensus size: 6

        742 CGTTAACGGA

                                                        
        752 TGATTG TGATTG TGATTG TGA-TG TGATTG TGATTG TG
          1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG

        789 GTGCAGCCTG


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   5    5  0.17
   6   25  0.83

ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49


Consensus pattern (6 bp):   
TGATTG

Found at i:778 original size:11 final size:11

Alignment explanation


    Indices: 752--784  Score: 57
    Period size: 11  Copynumber: 2.9  Consensus size: 11

        742 CGTTAACGGA

                        
        752 TGATTGTGATTG
          1 TGATTGTGA-TG

                       
        764 TGATTGTGATG
          1 TGATTGTGATG

                      
        775 TGATTGTGAT
          1 TGATTGTGAT

        785 TGTGGTGCAG


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

Matches are distributed among these distances:
  11   12  0.57
  12    9  0.43

ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48


Consensus pattern (11 bp):   
TGATTGTGATG

Found at i:778 original size:17 final size:17

Alignment explanation


    Indices: 756--788  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        746 AACGGATGAT

                             
        756 TGTGATTGTGATTGTGA
          1 TGTGATTGTGATTGTGA

                            
        773 TGTGATTGTGATTGTG
          1 TGTGATTGTGATTGTG

        789 GTGCAGCCTG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.15, C:0.00, G:0.36, T:0.48


Consensus pattern (17 bp):   
TGTGATTGTGATTGTGA
Done.