Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006810.1 Corchorus olitorius cultivar O-4 contig06835, 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, 852

Length: 1420
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29


Found at i:292 original size:2 final size:2

Alignment explanation


    Indices: 285--329  Score: 81
    Period size: 2  Copynumber: 22.5  Consensus size: 2

        275 AAATTACTAG

                                                               *          
        285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                
        327 TA T
          1 TA T

        330 GTTCGCGCCA


Statistics
Matches: 41,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   41  1.00

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:487 original size:50 final size:48

Alignment explanation


    Indices: 385--527  Score: 168
    Period size: 49  Copynumber: 3.0  Consensus size: 48

        375 GAGCGTGCCA

                                   *                  * *    
        385 ATCAATTTTGTC-AAAAAATTGATAAAAAGTGCAA-TGAAAATTCAAAG
          1 ATCAATTTTGTCTAAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG

                                                              
        432 ATCAATTTTGTCTTAAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG

            *           *                                   
        482 TTCAATTTTGTAGT-AAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAA
          1 ATCAATTTTGT-CTAAAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAA

        528 GGATTGCTTT


Statistics
Matches: 85,  Mismatches: 5, Indels: 11
        0.84            0.05        0.11

Matches are distributed among these distances:
  47   20  0.24
  48    7  0.08
  49   32  0.38
  50   25  0.29
  51    1  0.01

ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27


Consensus pattern (48 bp):   
ATCAATTTTGTCTAAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Done.