Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001393.1 Corchorus olitorius cultivar O-4 contig01393, 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: 2174
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Found at i:1217 original size:22 final size:22

Alignment explanation


    Indices: 1175--1216  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1165 ATCTATTTAA

                                  
       1175 TATTTCTATTTCTTTATTTTTC
          1 TATTTCTATTTCTTTATTTTTC

                                 
       1197 TATTTCT-TTTCTTTATTTTT
          1 TATTTCTATTTCTTTATTTTT

       1217 TTCTGTCGAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  21   13  0.65
  22    7  0.35

ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76


Consensus pattern (22 bp):   
TATTTCTATTTCTTTATTTTTC

Found at i:2029 original size:5 final size:5

Alignment explanation


    Indices: 2019--2055  Score: 65
    Period size: 5  Copynumber: 7.4  Consensus size: 5

       2009 TGAGAGAAGG

                          *                             
       2019 AAAGA AAAGA AATGA AAAGA AAAGA AAAGA AAAGA AA
          1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA

       2056 GGGAAGGAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   5   30  1.00

ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03


Consensus pattern (5 bp):   
AAAGA

Found at i:2065 original size:15 final size:15

Alignment explanation


    Indices: 2015--2065  Score: 59
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       2005 CAAATGAGAG

                           
       2015 AAGG-AAAGAAAAGA
          1 AAGGAAAAGAAAAGA

              *            
       2029 AATGAAAAGAAAAGA
          1 AAGGAAAAGAAAAGA

              *         * *
       2044 AAAGAAAAGAAAGGG
          1 AAGGAAAAGAAAAGA

                   
       2059 AAGGAAA
          1 AAGGAAA

       2066 GGAACACCAC


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  14    3  0.10
  15   28  0.90

ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02


Consensus pattern (15 bp):   
AAGGAAAAGAAAAGA
Done.