Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021221.1 Corchorus olitorius cultivar O-4 contig21254, 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: 4557
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32


Found at i:1637 original size:66 final size:66

Alignment explanation


    Indices: 1556--1688  Score: 257
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       1546 TAATGACTGT

                                                                             
       1556 AGGTCCTCATGATAAAACATGTGGAAGTAGATGACCAAAAACACACTCATCACCTATACAGACCT
          1 AGGTCCTCATGATAAAACATGTGGAAGTAGATGACCAAAAACACACTCATCACCTATACAGACCT

             
       1621 C
         66 C

                                              *                              
       1622 AGGTCCTCATGATAAAACATGTGGAAGTAGATGATCAAAAACACACTCATCACCTATACAGACCT
          1 AGGTCCTCATGATAAAACATGTGGAAGTAGATGACCAAAAACACACTCATCACCTATACAGACCT

             
       1687 C
         66 C

             
       1688 A
          1 A

       1689 TATGTGGTGA


Statistics
Matches: 66,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  66   66  1.00

ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20


Consensus pattern (66 bp):   
AGGTCCTCATGATAAAACATGTGGAAGTAGATGACCAAAAACACACTCATCACCTATACAGACCT
C

Found at i:2824 original size:2 final size:2

Alignment explanation


    Indices: 2808--2842  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       2798 ACATACATAC

                            *                                    
       2808 AT AT AT A- AT AA AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2843 TTACATTTAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.97

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:4019 original size:6 final size:6

Alignment explanation


    Indices: 3969--4018  Score: 91
    Period size: 6  Copynumber: 8.3  Consensus size: 6

       3959 CAGGCTACAC

                                                               *   
       3969 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CATAAT
          1 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT

              
       4017 CA
          1 CA

       4019 TCCGTTAACG


Statistics
Matches: 43,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   6   43  1.00

ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18


Consensus pattern (6 bp):   
CACAAT

Found at i:4212 original size:39 final size:38

Alignment explanation


    Indices: 4048--4230  Score: 296
    Period size: 38  Copynumber: 4.8  Consensus size: 38

       4038 TCGAGTCTAG

                                                  
       4048 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                                                  
       4085 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                                                  
       4123 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                               *  * *              
       4161 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA

               *           *      *        
       4200 CCATCAGTTTAACCCTCTGAGGTACGGGTCC
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCC

       4231 GCTATGCACA


Statistics
Matches: 137,  Mismatches: 7, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
  37    7  0.05
  38  100  0.73
  39   30  0.22

ACGTcount: A:0.22, C:0.35, G:0.19, T:0.23


Consensus pattern (38 bp):   
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Done.