Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001350.1 Corchorus olitorius cultivar O-4 contig01350, 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: 7253
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30


Found at i:383 original size:12 final size:12

Alignment explanation


    Indices: 343--392  Score: 57
    Period size: 12  Copynumber: 3.9  Consensus size: 12

        333 TATTCAATTT

                        
        343 TTATATA-TATA
          1 TTATATATTATA

                            
        354 TTGATAATAATGTATA
          1 TT-AT-AT-AT-TATA

                        
        370 TTATATATTATA
          1 TTATATATTATA

                       
        382 TTATATATTAT
          1 TTATATATTAT

        393 CAATAAACTT


Statistics
Matches: 34,  Mismatches: 0, Indels: 9
        0.79            0.00        0.21

Matches are distributed among these distances:
  11    2  0.06
  12   17  0.50
  13    4  0.12
  14    3  0.09
  15    2  0.06
  16    6  0.18

ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54


Consensus pattern (12 bp):   
TTATATATTATA

Found at i:585 original size:16 final size:16

Alignment explanation


    Indices: 564--620  Score: 80
    Period size: 16  Copynumber: 3.6  Consensus size: 16

        554 CTACCCGAGA

                            
        564 CCGAACCCAAAAATAC
          1 CCGAACCCAAAAATAC

                     *       
        580 CCGAACCC-GAAATAAC
          1 CCGAACCCAAAAAT-AC

                    *       
        596 CCGAACCCGAAAATAC
          1 CCGAACCCAAAAATAC

                     
        612 CCGAACCCA
          1 CCGAACCCA

        621 CCCAATTGCC


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  15    4  0.11
  16   28  0.78
  17    4  0.11

ACGTcount: A:0.44, C:0.40, G:0.11, T:0.05


Consensus pattern (16 bp):   
CCGAACCCAAAAATAC

Found at i:5503 original size:29 final size:29

Alignment explanation


    Indices: 5457--5512  Score: 85
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       5447 ACATTTGCCG

                      * **               
       5457 AAATGCTCAATTTGGTGCCAAACCTTTGA
          1 AAATGCTCAAATCAGTGCCAAACCTTTGA

                                       
       5486 AAATGCTCAAATCAGTGCCAAACCTTT
          1 AAATGCTCAAATCAGTGCCAAACCTTT

       5513 CGGACTTGGT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29


Consensus pattern (29 bp):   
AAATGCTCAAATCAGTGCCAAACCTTTGA
Done.