Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016308.1 Corchorus olitorius cultivar O-4 contig16341, 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: 4665
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28


Found at i:4106 original size:13 final size:13

Alignment explanation


    Indices: 4031--4140  Score: 74
    Period size: 13  Copynumber: 8.8  Consensus size: 13

       4021 TGGTGGAAAA

                         
       4031 TTTGATGAAGAAC
          1 TTTGATGAAGAAC

                          
       4044 --TGAGTGAA-AAC
          1 TTTGA-TGAAGAAC

                *        
       4055 -TTGTTGAAGAAC
          1 TTTGATGAAGAAC

              *            
       4067 AACTTGATGAAG-AC
          1 --TTTGATGAAGAAC

                *        
       4081 -TTGTTGAAGAAC
          1 TTTGATGAAGAAC

                     *   
       4093 TTTGATGAATAAC
          1 TTTGATGAAGAAC

                * *      
       4106 TTTGGTAAAG-AC
          1 TTTGATGAAGAAC

                *        
       4118 -TTGTTGAAGAAC
          1 TTTGATGAAGAAC

                       
       4130 TTTGATGAAGA
          1 TTTGATGAAGA

       4141 CTTGTTTCAC


Statistics
Matches: 76,  Mismatches: 11, Indels: 20
        0.71            0.10        0.19

Matches are distributed among these distances:
  11   25  0.33
  12   15  0.20
  13   26  0.34
  14    2  0.03
  15    8  0.11

ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31


Consensus pattern (13 bp):   
TTTGATGAAGAAC

Found at i:4130 original size:24 final size:24

Alignment explanation


    Indices: 4098--4146  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       4088 AGAACTTTGA

                *       *           
       4098 TGAATAACTTTGGTAAAGACTTGT
          1 TGAAGAACTTTGATAAAGACTTGT

                          *         
       4122 TGAAGAACTTTGATGAAGACTTGT
          1 TGAAGAACTTTGATAAAGACTTGT

             
       4146 T
          1 T

       4147 TCACTCTTGG


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37


Consensus pattern (24 bp):   
TGAAGAACTTTGATAAAGACTTGT
Done.