Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024194.1 Corchorus olitorius cultivar O-4 contig24227, 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: 7217
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38


Found at i:2255 original size:36 final size:36

Alignment explanation


    Indices: 2208--2277  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       2198 GAGATTTTGG

                         *      *               
       2208 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
       2244 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       2278 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:5132 original size:2 final size:2

Alignment explanation


    Indices: 5125--5171  Score: 76
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       5115 CTATAACTAG

                                                             *             
       5125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA CTA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA

                 
       5168 TA TA
          1 TA TA

       5172 AGTCTAAACT


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   2   40  0.95
   3    2  0.05

ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:5344 original size:15 final size:17

Alignment explanation


    Indices: 5314--5345  Score: 50
    Period size: 15  Copynumber: 2.0  Consensus size: 17

       5304 TATCAATTAA

                             
       5314 ATTAAATATATTATAAT
          1 ATTAAATATATTATAAT

                             
       5331 ATTAAA-AT-TTATAAT
          1 ATTAAATATATTATAAT

       5346 TTCTTTTACC


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    7  0.47
  16    2  0.13
  17    6  0.40

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (17 bp):   
ATTAAATATATTATAAT

Found at i:6555 original size:36 final size:36

Alignment explanation


    Indices: 6508--6577  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       6498 GAGATTTTGG

                         *      *               
       6508 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
       6544 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       6578 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.