Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013759.1 Corchorus olitorius cultivar O-4 contig13792, 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: 25308
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1070 original size:13 final size:13

Alignment explanation


    Indices: 1028--1072  Score: 56
    Period size: 12  Copynumber: 3.5  Consensus size: 13

       1018 TCATGCACCC

                        * 
       1028 AAAACAATTTATTT
          1 AAAACAATTTA-AT

                 *       
       1042 AAAACCATTT-AT
          1 AAAACAATTTAAT

                         
       1054 AAAACAATTTAAT
          1 AAAACAATTTAAT

                  
       1067 AAAACA
          1 AAAACA

       1073 GTAATAAAAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  12   10  0.37
  13    8  0.30
  14    9  0.33

ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31


Consensus pattern (13 bp):   
AAAACAATTTAAT

Found at i:2620 original size:17 final size:16

Alignment explanation


    Indices: 2598--2641  Score: 63
    Period size: 17  Copynumber: 2.8  Consensus size: 16

       2588 ATGAGGCCCA

                            
       2598 CGCGCTGGCCTGGGCC
          1 CGCGCTGGCCTGGGCC

                        *    
       2614 GCGCGCTGGCCTAGGCC
          1 -CGCGCTGGCCTGGGCC

                        
       2631 CGC-CTGGCCTG
          1 CGCGCTGGCCTG

       2642 CTGGCTGGCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  15    7  0.28
  16    3  0.12
  17   15  0.60

ACGTcount: A:0.02, C:0.43, G:0.41, T:0.14


Consensus pattern (16 bp):   
CGCGCTGGCCTGGGCC

Found at i:4570 original size:17 final size:17

Alignment explanation


    Indices: 4550--4594  Score: 65
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       4540 TATGAACCGT

                          *   
       4550 TTTTTTCGGTAT-CTCTG
          1 TTTTTT-GGTATCCACTG

                             
       4567 TTTTTTGGTATCCACTG
          1 TTTTTTGGTATCCACTG

                       
       4584 TTTTTTGGTAT
          1 TTTTTTGGTAT

       4595 TATTTTGGTA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  16    5  0.19
  17   21  0.81

ACGTcount: A:0.09, C:0.13, G:0.18, T:0.60


Consensus pattern (17 bp):   
TTTTTTGGTATCCACTG

Found at i:5763 original size:27 final size:28

Alignment explanation


    Indices: 5708--5765  Score: 98
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       5698 CATATTAAGG

                      *                 
       5708 AAAAAATGCCTAAAGATGTAATGCAAAA
          1 AAAAAATGCCCAAAGATGTAATGCAAAA

                                  *     
       5736 AAAAAATGCCCAAAGATGTAATTCAAAA
          1 AAAAAATGCCCAAAGATGTAATGCAAAA

              
       5764 AA
          1 AA

       5766 GCTACCGATA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17


Consensus pattern (28 bp):   
AAAAAATGCCCAAAGATGTAATGCAAAA
Done.