Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019961.1 Corchorus olitorius cultivar O-4 contig19994, 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: 4217
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27


Found at i:3861 original size:18 final size:19

Alignment explanation


    Indices: 3830--3873  Score: 81
    Period size: 18  Copynumber: 2.4  Consensus size: 19

       3820 TAAATAATTT

                               
       3830 ATTTAATAACTAAAAATCA
          1 ATTTAATAACTAAAAATCA

                               
       3849 ATTTAAT-ACTAAAAATCA
          1 ATTTAATAACTAAAAATCA

                   
       3867 ATTTAAT
          1 ATTTAAT

       3874 TTATTTAATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  18   18  0.72
  19    7  0.28

ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36


Consensus pattern (19 bp):   
ATTTAATAACTAAAAATCA

Found at i:3877 original size:46 final size:47

Alignment explanation


    Indices: 3824--3920  Score: 171
    Period size: 46  Copynumber: 2.1  Consensus size: 47

       3814 ATAACATAAA

                                                            
       3824 TAATTTATTTAATAACTAAAAATCAATTTAATACT-A-AAAATCAATT
          1 TAATTTATTTAATAACTAAAAATCAATTTAAT-CTAATAAAATCAATT

                                                           
       3870 TAATTTATTTAATAACTAAAAATCAATTTAATCTAATAAAATCAATT
          1 TAATTTATTTAATAACTAAAAATCAATTTAATCTAATAAAATCAATT

                
       3917 TAAT
          1 TAAT

       3921 AACTGAAATT


Statistics
Matches: 49,  Mismatches: 0, Indels: 3
        0.94            0.00        0.06

Matches are distributed among these distances:
  45    2  0.04
  46   33  0.67
  47   14  0.29

ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40


Consensus pattern (47 bp):   
TAATTTATTTAATAACTAAAAATCAATTTAATCTAATAAAATCAATT

Found at i:3879 original size:27 final size:28

Alignment explanation


    Indices: 3849--3901  Score: 99
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       3839 CTAAAAATCA

                                        
       3849 ATTTAAT-ACTAAAAATCAATTTAATTT
          1 ATTTAATAACTAAAAATCAATTTAATTT

                                      
       3876 ATTTAATAACTAAAAATCAATTTAAT
          1 ATTTAATAACTAAAAATCAATTTAAT

       3902 CTAATAAAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  27    7  0.28
  28   18  0.72

ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42


Consensus pattern (28 bp):   
ATTTAATAACTAAAAATCAATTTAATTT

Found at i:3900 original size:19 final size:21

Alignment explanation


    Indices: 3876--3924  Score: 70
    Period size: 19  Copynumber: 2.5  Consensus size: 21

       3866 AATTTAATTT

                                 
       3876 ATTTAATAACT-A-AAAATCA
          1 ATTTAATAACTAATAAAATCA

                                 
       3895 ATTTAAT--CTAATAAAATCA
          1 ATTTAATAACTAATAAAATCA

                       
       3914 ATTTAATAACT
          1 ATTTAATAACT

       3925 GAAATTGTCA


Statistics
Matches: 26,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  17    2  0.08
  18    1  0.04
  19   21  0.81
  21    2  0.08

ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37


Consensus pattern (21 bp):   
ATTTAATAACTAATAAAATCA
Done.