Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015161.1 Corchorus olitorius cultivar O-4 contig15194, 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: 6570
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36


Found at i:2870 original size:2 final size:2

Alignment explanation


    Indices: 2863--2900  Score: 58
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       2853 ATATTATTAC

                                                    *               
       2863 TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T

       2901 TAAAAAGTAC


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   2   31  0.94
   3    2  0.06

ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:3189 original size:127 final size:123

Alignment explanation


    Indices: 3000--3244  Score: 319
    Period size: 135  Copynumber: 1.9  Consensus size: 123

       2990 TTATAGTTTC

                                                      *            **        
       3000 ACTCAACTAAAACTCTATATTTATATAATTAAATCTAATATCTTTATAATTTTTACCATTTTACT
          1 ACTCAACTAAAACTCTATATTTATATAATTAAATCTAATATCCTTATAATTTTTATAATTTTACT

                                                                      
       3065 ATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTGACAGTATT
         66 ATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTGACAGTATT

                               *          *                                 *
       3123 ACTCAACTAAAAACTCTATTTTTATTTAATTATTAAATCTAATATCCTTATACCTATTTTATTTT
          1 ACTCAACT-AAAACTCTATATTTA--T-ATAATTAAATCTAATATCCTTATA---A--TT-TTTA

                                                     *               
       3188 TACCATTTTACTATTTTAATTAAAAAAACTTATATATATTATAATTTTTTAAATATA
         56 TA--ATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATA

       3245 TTTTTTAAAT


Statistics
Matches: 103,  Mismatches: 7, Indels: 12
        0.84            0.06        0.10

Matches are distributed among these distances:
 123    8  0.08
 124   14  0.14
 126    1  0.01
 127   22  0.21
 130    1  0.01
 132    2  0.02
 133    3  0.03
 135   52  0.50

ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48


Consensus pattern (123 bp):   
ACTCAACTAAAACTCTATATTTATATAATTAAATCTAATATCCTTATAATTTTTATAATTTTACT
ATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTGACAGTATT

Found at i:3249 original size:13 final size:14

Alignment explanation


    Indices: 3231--3268  Score: 60
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       3221 ATATATTATA

                         *
       3231 ATTTTTTAAAT-AT
          1 ATTTTTTAAATGAC

                          
       3244 ATTTTTTAAATGAC
          1 ATTTTTTAAATGAC

                       
       3258 ATTTTTTAAAT
          1 ATTTTTTAAAT

       3269 TTTACAATTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  13   11  0.48
  14   12  0.52

ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58


Consensus pattern (14 bp):   
ATTTTTTAAATGAC

Found at i:4178 original size:7 final size:7

Alignment explanation


    Indices: 4168--4194  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

       4158 TTTTAAGGGT

                   
       4168 TAATATG
          1 TAATATG

                   
       4175 TAATATG
          1 TAATATG

                   
       4182 TAATATG
          1 TAATATG

                  
       4189 TAATAT
          1 TAATAT

       4195 ATATATTTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44


Consensus pattern (7 bp):   
TAATATG

Done.