Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001630.1 Corchorus olitorius cultivar O-4 contig01630, 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: 6069
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:3968 original size:17 final size:17

Alignment explanation


    Indices: 3946--3979  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       3936 CTCTTATAAA

                             
       3946 TTTCTTAATTCTATTTG
          1 TTTCTTAATTCTATTTG

                      *      
       3963 TTTCTTAATTTTATTTG
          1 TTTCTTAATTCTATTTG

       3980 GTTGGACGAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.18, C:0.09, G:0.06, T:0.68


Consensus pattern (17 bp):   
TTTCTTAATTCTATTTG

Found at i:5590 original size:16 final size:16

Alignment explanation


    Indices: 5550--5591  Score: 59
    Period size: 15  Copynumber: 2.7  Consensus size: 16

       5540 CAGGCTCGGG

                            
       5550 CGGATTCGGGTACTTT
          1 CGGATTCGGGTACTTT

               *        *   
       5566 -GGGTTCGGGTATTTT
          1 CGGATTCGGGTACTTT

                       
       5581 CGGATTCGGGT
          1 CGGATTCGGGT

       5592 TAAATCAGGT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

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

ACGTcount: A:0.10, C:0.14, G:0.38, T:0.38


Consensus pattern (16 bp):   
CGGATTCGGGTACTTT

Found at i:5760 original size:9 final size:9

Alignment explanation


    Indices: 5746--5800  Score: 60
    Period size: 9  Copynumber: 6.1  Consensus size: 9

       5736 AAGTTTATTG

                     
       5746 ATAATATAT
          1 ATAATATAT

                     
       5755 ATAATATAT
          1 ATAATATAT

                      
       5764 ATAATATACT
          1 ATAATATA-T

                *    
       5774 ATAACAT-T
          1 ATAATATAT

              *       
       5782 ATTATCA-AT
          1 ATAAT-ATAT

                     
       5791 ATAATATAT
          1 ATAATATAT

             
       5800 A
          1 A

       5801 AAAGATTGAA


Statistics
Matches: 38,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
   8    5  0.13
   9   26  0.68
  10    7  0.18

ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42


Consensus pattern (9 bp):   
ATAATATAT

Found at i:5784 original size:40 final size:41

Alignment explanation


    Indices: 5721--5798  Score: 97
    Period size: 40  Copynumber: 1.9  Consensus size: 41

       5711 TTTTATCTTT

                 *     *     **                       
       5721 TATATTATATATTATAAGTTTATTGAT-AATAT-ATATAATA
          1 TATATAATATACTATAACATTATT-ATCAATATAATATAATA

                                                  
       5761 TATATAATATACTATAACATTATTATCAATATAATATA
          1 TATATAATATACTATAACATTATTATCAATATAATATA

       5799 TAAAAGATTG


Statistics
Matches: 32,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  39    2  0.06
  40   25  0.78
  41    5  0.16

ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46


Consensus pattern (41 bp):   
TATATAATATACTATAACATTATTATCAATATAATATAATA
Done.