Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014530.1 Corchorus olitorius cultivar O-4 contig14563, 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: 5083
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:3887 original size:35 final size:35

Alignment explanation


    Indices: 3846--3920  Score: 134
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       3836 AGTTCGTTTA

                                                
       3846 TGTTCACGAACA-AGCTCGTTTATTGTTCATTTAAG
          1 TGTTCACGAACAGA-CTCGTTTATTGTTCATTTAAG

                                               
       3881 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
          1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

                 
       3916 TGTTC
          1 TGTTC

       3921 GTTTATATAA


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

Matches are distributed among these distances:
  35   38  0.97
  36    1  0.03

ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41


Consensus pattern (35 bp):   
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG

Found at i:3983 original size:16 final size:16

Alignment explanation


    Indices: 3962--3993  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       3952 TATAATTATT

                            
       3962 TATATATTAATAATAA
          1 TATATATTAATAATAA

                     *      
       3978 TATATATTATTAATAA
          1 TATATATTAATAATAA

       3994 AAATAATAAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (16 bp):   
TATATATTAATAATAA

Found at i:3988 original size:19 final size:19

Alignment explanation


    Indices: 3946--3998  Score: 63
    Period size: 19  Copynumber: 2.8  Consensus size: 19

       3936 GAACGCTCGT

                        *  *    
       3946 TTATTATATAATTATTTATA
          1 TTATTA-ATAATAATATATA

                               
       3966 -TATTAATAATAATATATA
          1 TTATTAATAATAATATATA

                      *    
       3984 TTATTAATAAAAATA
          1 TTATTAATAATAATA

       3999 ATAATATTCT


Statistics
Matches: 29,  Mismatches: 3, Indels: 3
        0.83            0.09        0.09

Matches are distributed among these distances:
  18   11  0.38
  19   18  0.62

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (19 bp):   
TTATTAATAATAATATATA

Found at i:4000 original size:25 final size:27

Alignment explanation


    Indices: 3970--4019  Score: 77
    Period size: 25  Copynumber: 1.9  Consensus size: 27

       3960 TTTATATATT

                                       
       3970 AATAATAATA-TATATTAT-TAATAAA
          1 AATAATAATATTATATTATCTAATAAA

                        *            
       3995 AATAATAATATTCTATTATCTAATA
          1 AATAATAATATTATATTATCTAATA

       4020 TATTTAAATG


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  25   10  0.45
  26    7  0.32
  27    5  0.23

ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42


Consensus pattern (27 bp):   
AATAATAATATTATATTATCTAATAAA

Found at i:4139 original size:18 final size:18

Alignment explanation


    Indices: 4112--4146  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       4102 AATTATTACA

                              
       4112 TTGTTCATGAACAATTTT
          1 TTGTTCATGAACAATTTT

                 *           
       4130 TTGTTTATGAACAATTT
          1 TTGTTCATGAACAATTT

       4147 CAATTTTTGT


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

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51


Consensus pattern (18 bp):   
TTGTTCATGAACAATTTT
Done.