Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020834.1 Corchorus olitorius cultivar O-4 contig20867, 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: 33094
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:12680 original size:4 final size:4

Alignment explanation


    Indices: 12673--12709  Score: 74
    Period size: 4  Copynumber: 9.2  Consensus size: 4

      12663 TATATATATA

                                                          
      12673 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
          1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T

      12710 TGGAGTAAAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   33  1.00

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (4 bp):   
TATT

Found at i:21734 original size:30 final size:31

Alignment explanation


    Indices: 21698--21760  Score: 101
    Period size: 33  Copynumber: 2.0  Consensus size: 31

      21688 CATATTGGCT

                                           
      21698 TTGTATTTC-TCAGCTTCTTTTGGCATGCCA
          1 TTGTATTTCATCAGCTTCTTTTGGCATGCCA

                                             
      21728 TTGTATTTCTGATCAGCTTCTTTTGGCATGCCA
          1 TTGTATTTC--ATCAGCTTCTTTTGGCATGCCA

      21761 AGAAACCCGC


Statistics
Matches: 30,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  30    9  0.30
  33   21  0.70

ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46


Consensus pattern (31 bp):   
TTGTATTTCATCAGCTTCTTTTGGCATGCCA

Found at i:27574 original size:21 final size:21

Alignment explanation


    Indices: 27549--27595  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      27539 CACATTCACT

                                 
      27549 TGGTGAAGGAGACGGCGGTGG
          1 TGGTGAAGGAGACGGCGGTGG

                 *   *  *        
      27570 TGGTGGAGGTGATGGCGGTGG
          1 TGGTGAAGGAGACGGCGGTGG

            *    
      27591 CGGTG
          1 TGGTG

      27596 GTGGTGGAGG


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.13, C:0.09, G:0.60, T:0.19


Consensus pattern (21 bp):   
TGGTGAAGGAGACGGCGGTGG

Found at i:27596 original size:21 final size:21

Alignment explanation


    Indices: 27562--27601  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      27552 TGAAGGAGAC

                    *            
      27562 GGCGGTGGTGGTGGAGGTGAT
          1 GGCGGTGGCGGTGGAGGTGAT

                          *    
      27583 GGCGGTGGCGGTGGTGGTG
          1 GGCGGTGGCGGTGGAGGTG

      27602 GAGGAACACT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.05, C:0.07, G:0.65, T:0.23


Consensus pattern (21 bp):   
GGCGGTGGCGGTGGAGGTGAT
Done.