Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020179.1 Corchorus olitorius cultivar O-4 contig20212, 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: 14183
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:10741 original size:15 final size:16

Alignment explanation


    Indices: 10708--10747  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      10698 TTACTTTGCT

                            
      10708 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
      10724 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
      10739 TTGCTTTCT
          1 TTGTTTTCT

      10748 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:11890 original size:24 final size:24

Alignment explanation


    Indices: 11845--11890  Score: 58
    Period size: 24  Copynumber: 1.9  Consensus size: 24

      11835 TTTTCTATGA

                          *  *      
      11845 AATTTAAAAAATATTATTTTATAT
          1 AATTTAAAAAATATAATATTATAT

                                   
      11869 AATTTAAAAAA-ACTAATATTAT
          1 AATTTAAAAAATA-TAATATTAT

      11891 TATTTTGAAC


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  23    1  0.05
  24   18  0.95

ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43


Consensus pattern (24 bp):   
AATTTAAAAAATATAATATTATAT

Found at i:13518 original size:61 final size:61

Alignment explanation


    Indices: 13387--13503  Score: 162
    Period size: 61  Copynumber: 1.9  Consensus size: 61

      13377 TTGGACCCTT

                    *                         * *            **          
      13387 ATTTGAGCTTTTTTTTTTCTTTGGACACTTATTTGAGCACTTTCGCAAATGTTGGGTCCTA
          1 ATTTGAGCATTTTTTTTTCTTTGGACACTTATTTAAACACTTTCGCAAACATTGGGTCCTA

                                    * *            *                
      13448 ATTTGAGCATTTTTTTTTCTTTGGGCCCTTATTTAAACATTTTCGCAAACATTGGG
          1 ATTTGAGCATTTTTTTTTCTTTGGACACTTATTTAAACACTTTCGCAAACATTGGG

      13504 CACTTTTTTG


Statistics
Matches: 48,  Mismatches: 8, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  61   48  1.00

ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47


Consensus pattern (61 bp):   
ATTTGAGCATTTTTTTTTCTTTGGACACTTATTTAAACACTTTCGCAAACATTGGGTCCTA

Found at i:13850 original size:136 final size:136

Alignment explanation


    Indices: 13606--13878  Score: 519
    Period size: 136  Copynumber: 2.0  Consensus size: 136

      13596 CATTGCACTA

                                                                       *     
      13606 ATTAATATACTTTATTTCTTAAATTAATATAAGTCAAAACAATTAAATTATTTATTCAAGATTTA
          1 ATTAATATACTTTATTTCTTAAATTAATATAAGTCAAAACAATTAAATTATTTATTCAAAATTTA

                                                                             
      13671 TATATATTATGGATATAATAGTAACATCTTTTTCTAGTAAGAAGTATATTTAGCTACATTCTTTA
         66 TATATATTATGGATATAATAGTAACATCTTTTTCTAGTAAGAAGTATATTTAGCTACATTCTTTA

                  
      13736 AAACAT
        131 AAACAT

                                                *                            
      13742 ATTAATATACTTTATTTCTTAAATTAATATAAGTCAGAACAATTAAATTATTTATTCAAAATTTA
          1 ATTAATATACTTTATTTCTTAAATTAATATAAGTCAAAACAATTAAATTATTTATTCAAAATTTA

                                               *                             
      13807 TATATATTATGGATATAATAGTAACATCTTTTTCTGGTAAGAAGTATATTTAGCTACATTCTTTA
         66 TATATATTATGGATATAATAGTAACATCTTTTTCTAGTAAGAAGTATATTTAGCTACATTCTTTA

                  
      13872 AAACAT
        131 AAACAT

             
      13878 A
          1 A

      13879 ATTGTCTAGT


Statistics
Matches: 134,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 136  134  1.00

ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43


Consensus pattern (136 bp):   
ATTAATATACTTTATTTCTTAAATTAATATAAGTCAAAACAATTAAATTATTTATTCAAAATTTA
TATATATTATGGATATAATAGTAACATCTTTTTCTAGTAAGAAGTATATTTAGCTACATTCTTTA
AAACAT

Done.