Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021020.1 Corchorus olitorius cultivar O-4 contig21053, 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: 16455
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30


Found at i:3844 original size:2 final size:2

Alignment explanation


    Indices: 3837--3878  Score: 77
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       3827 TCATTGCAAG

                                                                          
       3837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             
       3878 A
          1 A

       3879 GTAATGTCAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   38  0.97

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


Consensus pattern (2 bp):   
AT

Found at i:4698 original size:38 final size:38

Alignment explanation


    Indices: 4647--4723  Score: 145
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       4637 TTAATAAAGT

                                                  
       4647 TCTATTACATAGGTACTTCATATTCAGCATTTTTATAC
          1 TCTATTACATAGGTACTTCATATTCAGCATTTTTATAC

                                              *   
       4685 TCTATTACATAGGTACTTCATATTCAGCATTTTTGTAC
          1 TCTATTACATAGGTACTTCATATTCAGCATTTTTATAC

             
       4723 T
          1 T

       4724 GATATACTTC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  38   38  1.00

ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45


Consensus pattern (38 bp):   
TCTATTACATAGGTACTTCATATTCAGCATTTTTATAC

Found at i:6207 original size:21 final size:21

Alignment explanation


    Indices: 6181--6223  Score: 70
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6171 ATTCCTCTAA

                                  
       6181 AATCAT-TAACAGAACATTCTT
          1 AATCATAT-ACAGAACATTCTT

                                 
       6202 AATCATATACAGAACATTCTT
          1 AATCATATACAGAACATTCTT

             
       6223 A
          1 A

       6224 GTGTAATTAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  21   20  0.95
  22    1  0.05

ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33


Consensus pattern (21 bp):   
AATCATATACAGAACATTCTT

Found at i:15185 original size:12 final size:11

Alignment explanation


    Indices: 15166--15216  Score: 52
    Period size: 12  Copynumber: 4.6  Consensus size: 11

      15156 CTAAACAGAG

                       
      15166 GTTTTTTTTTT
          1 GTTTTTTTTTT

                *      
      15177 G--TCTTTTTT
          1 GTTTTTTTTTT

                  *     
      15186 GTTTTCGTTTTT
          1 GTTTT-TTTTTT

                       
      15198 GTTTTTTTTTT
          1 GTTTTTTTTTT

                    
      15209 GCTTTTTT
          1 G-TTTTTT

      15217 GGGTACTAGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 7
        0.74            0.09        0.16

Matches are distributed among these distances:
   9    8  0.25
  11    8  0.25
  12   16  0.50

ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82


Consensus pattern (11 bp):   
GTTTTTTTTTT

Found at i:16424 original size:13 final size:14

Alignment explanation


    Indices: 16406--16438  Score: 50
    Period size: 13  Copynumber: 2.4  Consensus size: 14

      16396 TTACAGTATT

                          
      16406 AAAAAAAA-GAAAA
          1 AAAAAAAATGAAAA

                          
      16419 AAAAAAAATGAAAA
          1 AAAAAAAATGAAAA

                  
      16433 AGAAAA
          1 A-AAAA

      16439 TTGATCACTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  13    8  0.44
  14    6  0.33
  15    4  0.22

ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03


Consensus pattern (14 bp):   
AAAAAAAATGAAAA

Found at i:16425 original size:14 final size:15

Alignment explanation


    Indices: 16406--16438  Score: 50
    Period size: 14  Copynumber: 2.3  Consensus size: 15

      16396 TTACAGTATT

                           
      16406 AAAAAAAAGAAAAA-
          1 AAAAAAAAGAAAAAG

                   *       
      16420 AAAAAAATGAAAAAG
          1 AAAAAAAAGAAAAAG

                
      16435 AAAA
          1 AAAA

      16439 TTGATCACTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14   13  0.76
  15    4  0.24

ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03


Consensus pattern (15 bp):   
AAAAAAAAGAAAAAG
Done.