Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022014.1 Corchorus olitorius cultivar O-4 contig22047, 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: 12282
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33


Found at i:3404 original size:2 final size:2

Alignment explanation


    Indices: 3399--3431  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       3389 TGTGTGTGTG

                                                              
       3399 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       3432 AGCATTTTGT


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

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.97

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


Consensus pattern (2 bp):   
TA

Found at i:4536 original size:22 final size:22

Alignment explanation


    Indices: 4508--4549  Score: 84
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       4498 AAGAGAATCA

                                  
       4508 TCACAACCATAAATACATTGGC
          1 TCACAACCATAAATACATTGGC

                                
       4530 TCACAACCATAAATACATTG
          1 TCACAACCATAAATACATTG

       4550 TCAAGACAAG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24


Consensus pattern (22 bp):   
TCACAACCATAAATACATTGGC

Found at i:4955 original size:13 final size:13

Alignment explanation


    Indices: 4937--4961  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       4927 AATGCTTCTA

                         
       4937 AATAAAGTGTTCG
          1 AATAAAGTGTTCG

                        
       4950 AATAAAGTGTTC
          1 AATAAAGTGTTC

       4962 AAGTATAAGA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32


Consensus pattern (13 bp):   
AATAAAGTGTTCG
Done.