Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019224.1 Corchorus olitorius cultivar O-4 contig19257, 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: 35752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:5685 original size:4 final size:4

Alignment explanation


    Indices: 5676--5712  Score: 56
    Period size: 4  Copynumber: 8.8  Consensus size: 4

       5666 AATATACAAA

                                                         
       5676 AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AAAAT AAA
          1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAA

       5713 AACAAGGTAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   4   23  0.72
   5    9  0.28

ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22


Consensus pattern (4 bp):   
AAAT

Found at i:10901 original size:130 final size:131

Alignment explanation


    Indices: 10747--11009  Score: 384
    Period size: 130  Copynumber: 2.0  Consensus size: 131

      10737 GTCATTTAAG

                      *    *  *        *                 *       *           
      10747 AAATATATTTTAAAATTTCTAATATATCTAAGTTTTTTAACTAAATTAGTAAATTGATAAAAATA
          1 AAATATATTTAAAAAATTATAATATATATAAGTTTTTTAACTAAAATAGTAAAATGATAAAAATA

                                            *                                
      10812 AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA
         66 AAATAGGTATAAGGATATTAGATTTAATTAAACAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA

             
      10877 A
        131 A

                                           *        *               *       *
      10878 AAAT-TATTTAAAAAATTATAATATATATAATTTTTTTAATTAAAATAGTAAAATGGTAAAAATT
          1 AAATATATTTAAAAAATTATAATATATATAAGTTTTTTAACTAAAATAGTAAAATGATAAAAATA

                  *             *                 *          *               
      10942 AAATAGTTATAAGGATATTATATTTAATTAAACAAAAATAGAGTTTTTATTTGAGTAAAACTATA
         66 AAATAGGTATAAGGATATTAGATTTAATTAAACAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA

             
      11007 A
        131 A

              
      11008 AA
          1 AA

      11010 GTCTAAACAA


Statistics
Matches: 117,  Mismatches: 15, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
 130  113  0.97
 131    4  0.03

ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39


Consensus pattern (131 bp):   
AAATATATTTAAAAAATTATAATATATATAAGTTTTTTAACTAAAATAGTAAAATGATAAAAATA
AAATAGGTATAAGGATATTAGATTTAATTAAACAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA
A

Found at i:18256 original size:14 final size:14

Alignment explanation


    Indices: 18234--18263  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      18224 CTCCTCCTCC

                          
      18234 TTTTCTTTCCTCTT
          1 TTTTCTTTCCTCTT

                *         
      18248 TTTTTTTTCCTCTT
          1 TTTTCTTTCCTCTT

              
      18262 TT
          1 TT

      18264 CTCCTTGCTT


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (14 bp):   
TTTTCTTTCCTCTT
Done.