Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009552.1 Corchorus olitorius cultivar O-4 contig09584, 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: 11121
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:1946 original size:29 final size:28

Alignment explanation


    Indices: 1906--1968  Score: 81
    Period size: 29  Copynumber: 2.2  Consensus size: 28

       1896 TCATAAAAGG

                                        
       1906 AAAATTATTTTAAGAAGCTAAAAAGAAA
          1 AAAATTATTTTAAGAAGCTAAAAAGAAA

                   *       *  *    *     
       1934 AAGAATTGTTTTAAGGAGTTAAAGAGAAA
          1 AA-AATTATTTTAAGAAGCTAAAAAGAAA

                  
       1963 AAAATT
          1 AAAATT

       1969 CAACGAAATG


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  28    6  0.20
  29   24  0.80

ACGTcount: A:0.56, C:0.02, G:0.16, T:0.27


Consensus pattern (28 bp):   
AAAATTATTTTAAGAAGCTAAAAAGAAA

Found at i:2282 original size:75 final size:78

Alignment explanation


    Indices: 2137--2292  Score: 174
    Period size: 75  Copynumber: 2.0  Consensus size: 78

       2127 AAATTTTTAG

                             *        *                                      
       2137 GGGGCCAAATTATAAATCTTCCAGTTTTTTTTTTCATTTACTTGAAAAGCATAAATATGAAAGAA
          1 GGGGCCAAATTATAAATATTCCA--TATTTTTTTCATTTAC-T-AAAAGCATAAATATGAAAGAA

                   *  *      
       2202 ATCTTGGTAATTTGGGA
         62 ATCTTGGCAAATTGGGA

                                                       *     **      *   *   
       2219 GGGGCCAAATTATAAATATTCCA-ATTTTTTTCATTT-C-AAATGCATATGTATGAAGGAATTCT
          1 GGGGCCAAATTATAAATATTCCATATTTTTTTCATTTACTAAAAGCATAAATATGAAAGAAATCT

                        
       2281 TGGCAAATTGGG
         66 TGGCAAATTGGG

       2293 GGCCATGGCC


Statistics
Matches: 65,  Mismatches: 9, Indels: 7
        0.80            0.11        0.09

Matches are distributed among these distances:
  75   30  0.46
  78    1  0.02
  79   12  0.18
  82   22  0.34

ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37


Consensus pattern (78 bp):   
GGGGCCAAATTATAAATATTCCATATTTTTTTCATTTACTAAAAGCATAAATATGAAAGAAATCT
TGGCAAATTGGGA

Found at i:4357 original size:2 final size:2

Alignment explanation


    Indices: 4350--4384  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       4340 AAATCCTTGG

                                                                
       4350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4385 GTAATTATTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
TA

Done.