Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022585.1 Corchorus olitorius cultivar O-4 contig22618, 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: 11796
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:8162 original size:38 final size:38

Alignment explanation


    Indices: 8115--8221  Score: 162
    Period size: 39  Copynumber: 2.8  Consensus size: 38

       8105 ATGTTTTTAA

                *                                 
       8115 TTAAATAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
          1 TTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGT

               *                                   
       8153 TTAGGTAATTCCAAAAGAAGATTTTGGAAAAATAAAAGT
          1 TTAAGTAATTCCAAAAGAAGATTTTGG-AAAATAAAAGT

                      *                    
       8192 TTAAG-ATATCCCAAAAGAAGATTTTGGAAA
          1 TTAAGTA-ATTCCAAAAGAAGATTTTGGAAA

       8222 TTAATAAAAT


Statistics
Matches: 63,  Mismatches: 4, Indels: 4
        0.89            0.06        0.06

Matches are distributed among these distances:
  38   29  0.46
  39   34  0.54

ACGTcount: A:0.50, C:0.07, G:0.16, T:0.28


Consensus pattern (38 bp):   
TTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGT

Found at i:10327 original size:15 final size:15

Alignment explanation


    Indices: 10307--10348  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      10297 ACAGAGATTG

                           
      10307 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                    *      
      10322 ACAGAAAAAAATTAA
          1 ACAGAAAACAATTAA

                        
      10337 ACTAGAAAACAA
          1 AC-AGAAAACAA

      10349 AGCAAAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.69, C:0.12, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:11124 original size:11 final size:11

Alignment explanation


    Indices: 11108--11133  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

      11098 CCTTTGCCTA

                       
      11108 AAAACTAGAAG
          1 AAAACTAGAAG

                       
      11119 AAAACTAGAAG
          1 AAAACTAGAAG

                
      11130 AAAA
          1 AAAA

      11134 GAAATTATCC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG
Done.