Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011853.1 Corchorus olitorius cultivar O-4 contig11886, 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: 9312
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32


Found at i:1743 original size:21 final size:21

Alignment explanation


    Indices: 1717--1760  Score: 79
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1707 CAAAAATACC

                                 
       1717 ATGCAACTTACGGTGAACAAA
          1 ATGCAACTTACGGTGAACAAA

                              *  
       1738 ATGCAACTTACGGTGAACGAA
          1 ATGCAACTTACGGTGAACAAA

              
       1759 AT
          1 AT

       1761 AGAGACAAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20


Consensus pattern (21 bp):   
ATGCAACTTACGGTGAACAAA

Found at i:2086 original size:2 final size:2

Alignment explanation


    Indices: 2079--2117  Score: 60
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       2069 GAACTGTAGA

                                                      *      *        
       2079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AC AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2118 AGGGAAAGCA


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:7508 original size:21 final size:22

Alignment explanation


    Indices: 7484--7527  Score: 63
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       7474 TGTTTGCTAT

                          *       
       7484 CTTCCTCTTCC-TCGACTCAAA
          1 CTTCCTCTTCCTTCCACTCAAA

                *                 
       7505 CTTCTTCTTCCTTCCACTCAAA
          1 CTTCCTCTTCCTTCCACTCAAA

             
       7527 C
          1 C

       7528 CCTAGATCTC


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  21   10  0.50
  22   10  0.50

ACGTcount: A:0.18, C:0.43, G:0.02, T:0.36


Consensus pattern (22 bp):   
CTTCCTCTTCCTTCCACTCAAA

Done.