Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016075.1 Corchorus olitorius cultivar O-4 contig16108, 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: 5004
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30


Found at i:3679 original size:29 final size:28

Alignment explanation


    Indices: 3647--3702  Score: 94
    Period size: 29  Copynumber: 2.0  Consensus size: 28

       3637 CAGGAACAAG

                         *               
       3647 AAATTTTTTTTTTTAGAAAACGCAAAACA
          1 AAATTTTTTTTTTCA-AAAACGCAAAACA

                                       
       3676 AAATTTTTTTTTTCAAAAACGCAAAAC
          1 AAATTTTTTTTTTCAAAAACGCAAAAC

       3703 TAATAAATTA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  28   12  0.46
  29   14  0.54

ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38


Consensus pattern (28 bp):   
AAATTTTTTTTTTCAAAAACGCAAAACA

Found at i:4193 original size:15 final size:16

Alignment explanation


    Indices: 4175--4212  Score: 69
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       4165 AGATTGACAA

                            
       4175 AAAACAATTAAAC-AG
          1 AAAACAATTAAACTAG

                            
       4190 AAAACAATTAAACTAG
          1 AAAACAATTAAACTAG

                   
       4206 AAAACAA
          1 AAAACAA

       4213 AGCAAAGTAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.68, C:0.13, G:0.05, T:0.13


Consensus pattern (16 bp):   
AAAACAATTAAACTAG

Done.