Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023475.1 Corchorus olitorius cultivar O-4 contig23508, 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: 8262
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:3387 original size:51 final size:52

Alignment explanation


    Indices: 3286--3387  Score: 120
    Period size: 51  Copynumber: 2.0  Consensus size: 52

       3276 GTTCATCACA

                                                     * **       
       3286 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
          1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT

                                     *     *                     
       3338 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
          1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT

       3388 CTTCATTCAG


Statistics
Matches: 43,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  50    2  0.05
  51   36  0.84
  52    5  0.12

ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40


Consensus pattern (52 bp):   
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT

Found at i:5294 original size:12 final size:12

Alignment explanation


    Indices: 5277--5317  Score: 57
    Period size: 12  Copynumber: 3.4  Consensus size: 12

       5267 AAGAAATCAT

                        
       5277 GTTTTTATTTTA
          1 GTTTTTATTTTA

                        
       5289 GTTTTTATTTTA
          1 GTTTTTATTTTA

                       * 
       5301 GTTTATT-TTTAA
          1 GTTT-TTATTTTA

                 
       5313 GTTTT
          1 GTTTT

       5318 GTTTTGATTA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  11    1  0.04
  12   24  0.89
  13    2  0.07

ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73


Consensus pattern (12 bp):   
GTTTTTATTTTA

Found at i:6959 original size:2 final size:2

Alignment explanation


    Indices: 6952--6984  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       6942 ATAAGTAATC

                                                             
       6952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       6985 CTTCCACTCA


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

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.