Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017069.1 Corchorus olitorius cultivar O-4 contig17102, 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: 11343
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:8689 original size:73 final size:73

Alignment explanation


    Indices: 8593--8732  Score: 208
    Period size: 73  Copynumber: 1.9  Consensus size: 73

       8583 GGAAAATGGA

                             *               * *                    *        
       8593 CCATTTCAGTCGGCTAACACAGAAGTTGAAAACGCGCTGCCTATTGTGCCCATTCTGCATAAACA
          1 CCATTTCAGTCGGCTAAAACAGAAGTTGAAAACACCCTGCCTATTGTGCCCATTCTACATAAACA

                    
       8658 GTGAATTG
         66 GTGAATTG

                  *   *                               *           *          
       8666 CCATTTTAGTTGGCTAAAACAGAAGTTGAAAACACCCTGCCTGTTGTGCCCATTTTACATAAACA
          1 CCATTTCAGTCGGCTAAAACAGAAGTTGAAAACACCCTGCCTATTGTGCCCATTCTACATAAACA

              
       8731 GT
         66 GT

       8733 AAAATGCAGT


Statistics
Matches: 59,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  73   59  1.00

ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28


Consensus pattern (73 bp):   
CCATTTCAGTCGGCTAAAACAGAAGTTGAAAACACCCTGCCTATTGTGCCCATTCTACATAAACA
GTGAATTG

Found at i:10936 original size:3 final size:3

Alignment explanation


    Indices: 10928--10972  Score: 90
    Period size: 3  Copynumber: 15.0  Consensus size: 3

      10918 AGACTAAAAC

                                                                       
      10928 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA

      10973 AGTAGATTGA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   42  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:11031 original size:45 final size:41

Alignment explanation


    Indices: 10961--11043  Score: 103
    Period size: 44  Copynumber: 1.9  Consensus size: 41

      10951 AGAAGAAGAA

                         *    *           *           
      10961 GAAGAAGAAGAAAGTAGATTGAAATTTACCGATTAAAACGAG
          1 GAAGAAGAAGAAAATAGAATGAAA-TTACCAATTAAAACGAG

                                                     
      11003 GAAGAAGAAGAAAATAAAGAATGTAAATTACCAATTAAAAC
          1 GAAGAAGAAGAAAAT--AGAATG-AAATTACCAATTAAAAC

      11044 CTGGAAACAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  42   14  0.40
  44   18  0.51
  45    3  0.09

ACGTcount: A:0.55, C:0.07, G:0.19, T:0.18


Consensus pattern (41 bp):   
GAAGAAGAAGAAAATAGAATGAAATTACCAATTAAAACGAG
Done.