Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000592.1 Corchorus olitorius cultivar O-4 contig00592, 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: 1738
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38


Found at i:220 original size:50 final size:50

Alignment explanation


    Indices: 164--270  Score: 164
    Period size: 50  Copynumber: 2.2  Consensus size: 50

        154 TTTATAACTA

                               *                *   *          
        164 TTTTATTTTTACCATTTTATTATTTTAATTAAATATTTTTTTTAATAT-AC
          1 TTTTATTTTTACCATTTTACTATTTTAATTAAATATATTTCTTAA-ATGAC

                                                              
        214 TTTTATTTTTACCATTTTACTATTTTAATTAAATATATTTCTTAAATGAC
          1 TTTTATTTTTACCATTTTACTATTTTAATTAAATATATTTCTTAAATGAC

                    
        264 -TTTATTT
          1 TTTTATTT

        271 AAACTTTTAT


Statistics
Matches: 53,  Mismatches: 3, Indels: 3
        0.90            0.05        0.05

Matches are distributed among these distances:
  49    9  0.17
  50   44  0.83

ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62


Consensus pattern (50 bp):   
TTTTATTTTTACCATTTTACTATTTTAATTAAATATATTTCTTAAATGAC

Found at i:545 original size:32 final size:31

Alignment explanation


    Indices: 509--584  Score: 89
    Period size: 31  Copynumber: 2.4  Consensus size: 31

        499 ACTAAATACT

                      *                     
        509 AAAAAAGTTCTCTTATATTTTACTTTTGAGAC
          1 AAAAAAG-TCCCTTATATTTTACTTTTGAGAC

                           *    *      *   
        541 AAAAAAGTCCCTTATGTTTTTCTTTTGGGAC
          1 AAAAAAGTCCCTTATATTTTACTTTTGAGAC

               **        
        572 AAATCAGTCCCTT
          1 AAAAAAGTCCCTT

        585 GCTGACGTGG


Statistics
Matches: 38,  Mismatches: 6, Indels: 1
        0.84            0.13        0.02

Matches are distributed among these distances:
  31   31  0.82
  32    7  0.18

ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41


Consensus pattern (31 bp):   
AAAAAAGTCCCTTATATTTTACTTTTGAGAC
Done.