Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010011.1 Corchorus olitorius cultivar O-4 contig10043, 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: 12807
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:2444 original size:3 final size:3

Alignment explanation


    Indices: 2438--2465  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       2428 CTCTTTGATA

                                                 
       2438 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
          1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T

       2466 TCTTTTTTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TCT

Found at i:3944 original size:29 final size:29

Alignment explanation


    Indices: 3902--3979  Score: 147
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       3892 AAGTTGCAGT

                *                        
       3902 TGCTAATGATGAAGCTGCTAGAAAAATTG
          1 TGCTTATGATGAAGCTGCTAGAAAAATTG

                                         
       3931 TGCTTATGATGAAGCTGCTAGAAAAATTG
          1 TGCTTATGATGAAGCTGCTAGAAAAATTG

                                
       3960 TGCTTATGATGAAGCTGCTA
          1 TGCTTATGATGAAGCTGCTA

       3980 TGCTCTATAT


Statistics
Matches: 48,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  29   48  1.00

ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31


Consensus pattern (29 bp):   
TGCTTATGATGAAGCTGCTAGAAAAATTG

Found at i:7150 original size:7 final size:7

Alignment explanation


    Indices: 7138--7175  Score: 76
    Period size: 7  Copynumber: 5.4  Consensus size: 7

       7128 ATTTATTTAT

                   
       7138 GTGGGAA
          1 GTGGGAA

                   
       7145 GTGGGAA
          1 GTGGGAA

                   
       7152 GTGGGAA
          1 GTGGGAA

                   
       7159 GTGGGAA
          1 GTGGGAA

                   
       7166 GTGGGAA
          1 GTGGGAA

               
       7173 GTG
          1 GTG

       7176 AGGGATTCTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   31  1.00

ACGTcount: A:0.26, C:0.00, G:0.58, T:0.16


Consensus pattern (7 bp):   
GTGGGAA

Found at i:12778 original size:2 final size:2

Alignment explanation


    Indices: 12773--12807  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      12763 ACTTTTTTAT

                                                                
      12773 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.