Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016766.1 Corchorus olitorius cultivar O-4 contig16799, 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: 9684
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:5100 original size:20 final size:20

Alignment explanation


    Indices: 5059--5100  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       5049 GAGAAGTTAC

                             *  
       5059 AACTCACACATATAAAATAG
          1 AACTCACACATATAAAAGAG

                          *     
       5079 AACTCACACATATAGAAGAG
          1 AACTCACACATATAAAAGAG

              
       5099 AA
          1 AA

       5101 AGATACAAAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.55, C:0.19, G:0.10, T:0.17


Consensus pattern (20 bp):   
AACTCACACATATAAAAGAG

Found at i:5377 original size:2 final size:2

Alignment explanation


    Indices: 5370--5395  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       5360 GAAGCCATGA

                                                  
       5370 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       5396 GTGCTTTGGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:8079 original size:22 final size:22

Alignment explanation


    Indices: 8036--8087  Score: 59
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       8026 AATATTTTTA

                *        **       
       8036 TAAAATTTGATAACTACCCTAT
          1 TAAATTTTGATAAAAACCCTAT

                             *    
       8058 TAAATTTTGATAAAAACGCTAT
          1 TAAATTTTGATAAAAACCCTAT

            *       
       8080 AAAATTTT
          1 TAAATTTT

       8088 TTGATAATTA


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38


Consensus pattern (22 bp):   
TAAATTTTGATAAAAACCCTAT

Found at i:8115 original size:21 final size:20

Alignment explanation


    Indices: 8087--8153  Score: 64
    Period size: 22  Copynumber: 3.1  Consensus size: 20

       8077 TATAAAATTT

                                
       8087 TTTGATAATTATCTATGAAA
          1 TTTGATAATTATCTATGAAA

                                   
       8107 TTGTGATAAATT-TCATATGAAA
          1 TT-TGAT-AATTATC-TATGAAA

                      *  *        
       8129 CTTTGATAACCTAACTATGAAA
          1 -TTTGATAA-TTATCTATGAAA

               
       8151 TTT
          1 TTT

       8154 TGTAACCTTC


Statistics
Matches: 39,  Mismatches: 2, Indels: 11
        0.75            0.04        0.21

Matches are distributed among these distances:
  20    2  0.05
  21   11  0.28
  22   23  0.59
  23    3  0.08

ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42


Consensus pattern (20 bp):   
TTTGATAATTATCTATGAAA
Done.