Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022310.1 Corchorus olitorius cultivar O-4 contig22343, 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: 5815
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32


Found at i:3669 original size:16 final size:15

Alignment explanation


    Indices: 3628--3669  Score: 52
    Period size: 14  Copynumber: 2.8  Consensus size: 15

       3618 AACTAATCAG

                           
       3628 ATCATGACTCCACTA
          1 ATCATGACTCCACTA

                             
       3643 A-CAAT-ACTCCACTAA
          1 ATC-ATGACTCCACT-A

                        
       3658 ATCATGACTCCA
          1 ATCATGACTCCA

       3670 ATATCAGATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 7
        0.77            0.00        0.23

Matches are distributed among these distances:
  14    9  0.39
  15    7  0.30
  16    7  0.30

ACGTcount: A:0.38, C:0.33, G:0.05, T:0.24


Consensus pattern (15 bp):   
ATCATGACTCCACTA

Found at i:4647 original size:10 final size:10

Alignment explanation


    Indices: 4628--4679  Score: 59
    Period size: 10  Copynumber: 5.1  Consensus size: 10

       4618 TAGATGAGGT

                      
       4628 AAGAAAGGAA
          1 AAGAAAGGAA

               *      
       4638 AAGGAAGGAA
          1 AAGAAAGGAA

             *        
       4648 ATGAAAGGAA
          1 AAGAAAGGAA

                       
       4658 AAGAAAAGGAA
          1 AAG-AAAGGAA

             **       
       4669 ATCAAAGGAA
          1 AAGAAAGGAA

             
       4679 A
          1 A

       4680 GGAAGGGAAG


Statistics
Matches: 35,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  10   27  0.77
  11    8  0.23

ACGTcount: A:0.65, C:0.02, G:0.29, T:0.04


Consensus pattern (10 bp):   
AAGAAAGGAA

Found at i:4668 original size:21 final size:20

Alignment explanation


    Indices: 4630--4679  Score: 73
    Period size: 21  Copynumber: 2.5  Consensus size: 20

       4620 GATGAGGTAA

                       *        
       4630 GAAAGGAAAAGGAAGGAAAT
          1 GAAAGGAAAAGAAAGGAAAT

                                 
       4650 GAAAGGAAAAGAAAAGGAAAT
          1 GAAAGGAAAAG-AAAGGAAAT

            *        
       4671 CAAAGGAAA
          1 GAAAGGAAA

       4680 GGAAGGGAAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  20   11  0.41
  21   16  0.59

ACGTcount: A:0.64, C:0.02, G:0.30, T:0.04


Consensus pattern (20 bp):   
GAAAGGAAAAGAAAGGAAAT
Done.