Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000861.1 Corchorus olitorius cultivar O-4 contig00861, 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: 5519
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:272 original size:14 final size:15

Alignment explanation


    Indices: 253--287  Score: 56
    Period size: 14  Copynumber: 2.5  Consensus size: 15

        243 CCTTTTAAAT

                           
        253 TAAAATAG-TAAAAA
          1 TAAAATAGATAAAAA

                           
        267 TAAAAT-GATAAAAA
          1 TAAAATAGATAAAAA

                   
        281 TAAAATA
          1 TAAAATA

        288 ATTATAAAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  13    1  0.05
  14   18  0.95

ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23


Consensus pattern (15 bp):   
TAAAATAGATAAAAA

Found at i:586 original size:2 final size:2

Alignment explanation


    Indices: 562--608  Score: 67
    Period size: 2  Copynumber: 23.0  Consensus size: 2

        552 GTACTTTTTA

                          *        *                                       
        562 AT AT AGT AT AA AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                 
        605 AT AT
          1 AT AT

        609 TTTGCCCTAC


Statistics
Matches: 40,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
   2   38  0.95
   3    2  0.05

ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:5487 original size:2 final size:2

Alignment explanation


    Indices: 5480--5516  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       5470 GGAGATTACC

                                                                   
       5480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       5517 GTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.