Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017072.1 Corchorus olitorius cultivar O-4 contig17105, 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: 15554
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:8573 original size:9 final size:9

Alignment explanation


    Indices: 8559--8591  Score: 50
    Period size: 9  Copynumber: 3.7  Consensus size: 9

       8549 CTCTGCTGCT

                     
       8559 AGAAAAGAA
          1 AGAAAAGAA

                     
       8568 AGAAAAGAA
          1 AGAAAAGAA

                      
       8577 A-AAAATGAA
          1 AGAAAA-GAA

                  
       8586 AGAAAA
          1 AGAAAA

       8592 TGGAGTCCTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
   8    4  0.18
   9   14  0.64
  10    4  0.18

ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03


Consensus pattern (9 bp):   
AGAAAAGAA

Found at i:9003 original size:31 final size:30

Alignment explanation


    Indices: 8966--9028  Score: 108
    Period size: 31  Copynumber: 2.1  Consensus size: 30

       8956 GTTTGTTTGT

                         *                 
       8966 TGTGTGCAGTGTGTAAGGGTTGGTGTGACAG
          1 TGTGTGCAGTGTGCAAGGGTTGGTGTG-CAG

                                          
       8997 TGTGTGCAGTGTGCAAGGGTTGGTGTGCAG
          1 TGTGTGCAGTGTGCAAGGGTTGGTGTGCAG

              
       9027 TG
          1 TG

       9029 ACCTTGCCTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  30    5  0.16
  31   26  0.84

ACGTcount: A:0.14, C:0.08, G:0.46, T:0.32


Consensus pattern (30 bp):   
TGTGTGCAGTGTGCAAGGGTTGGTGTGCAG

Found at i:15274 original size:2 final size:2

Alignment explanation


    Indices: 15267--15346  Score: 66
    Period size: 2  Copynumber: 43.0  Consensus size: 2

      15257 CCGTTTAGTA

                                  *             *                        *
      15267 AT AT AT AT -T AT -T AA AT AT A- AT TT AT AT AT AT AT AT AT AA
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                   *                                       
      15306 AT AT AT A- AT AT AT CAG AT AT -T AT AT AT AT -T A- AT AT AT AT
          1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              
      15345 AT
          1 AT

      15347 TTGTAATAAT


Statistics
Matches: 62,  Mismatches: 8, Indels: 16
        0.72            0.09        0.19

Matches are distributed among these distances:
   1    7  0.11
   2   54  0.87
   3    1  0.02

ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:15438 original size:20 final size:20

Alignment explanation


    Indices: 15422--15462  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      15412 TTCTTCTTTC

                                
      15422 TCTCTCTTCTTCTTTCTTCT
          1 TCTCTCTTCTTCTTTCTTCT

                        *       
      15442 TCTCTCTTCTTCCTT-TTCT
          1 TCTCTCTTCTTCTTTCTTCT

              
      15461 TC
          1 TC

      15463 CATTTTTCGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  19    6  0.30
  20   14  0.70

ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63


Consensus pattern (20 bp):   
TCTCTCTTCTTCTTTCTTCT

Found at i:15439 original size:10 final size:10

Alignment explanation


    Indices: 15412--15462  Score: 50
    Period size: 10  Copynumber: 4.9  Consensus size: 10

      15402 TCTTTCCCTA

                       
      15412 TTCTTCTTTCT
          1 TTCTTC-TTCT

                        
      15423 CTCTCTTCTTCT
          1 -T-TCTTCTTCT

                      
      15435 TTCTTCTTCT
          1 TTCTTCTTCT

            *        *
      15445 CTCTTCTTCC
          1 TTCTTCTTCT

                     
      15455 TT-TTCTTC
          1 TTCTTCTTC

      15463 CATTTTTCGA


Statistics
Matches: 35,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
   9    6  0.17
  10   18  0.51
  11    1  0.03
  12    5  0.14
  13    5  0.14

ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65


Consensus pattern (10 bp):   
TTCTTCTTCT
Done.