Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017421.1 Corchorus olitorius cultivar O-4 contig17454, 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: 14065
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35


Found at i:2274 original size:31 final size:32

Alignment explanation


    Indices: 2219--2285  Score: 84
    Period size: 31  Copynumber: 2.1  Consensus size: 32

       2209 TTTTCTCTGA

                      *                     
       2219 TCATTCGGGTTTCGGCTCATCTGGATTCA-GG
          1 TCATTCGGGTCTCGGCTCATCTGGATTCAGGG

                           *            *    
       2250 TCATTCGGGTCTCGGGTC-TGCTGGATTTAGGG
          1 TCATTCGGGTCTCGGCTCAT-CTGGATTCAGGG

                
       2282 TCAT
          1 TCAT

       2286 GCAGGTTCGG


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  30    1  0.03
  31   24  0.77
  32    6  0.19

ACGTcount: A:0.12, C:0.21, G:0.31, T:0.36


Consensus pattern (32 bp):   
TCATTCGGGTCTCGGCTCATCTGGATTCAGGG

Found at i:2296 original size:31 final size:31

Alignment explanation


    Indices: 2239--2297  Score: 75
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       2229 TTCGGCTCAT

                           * *             
       2239 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
          1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG

                   *                     
       2270 CTGGATTTAGGGTCATGCAGGT-TCGGGT
          1 CTGGATTCA-GGTCATGCAGGTCTCGGGT

       2298 TTTCGCCTTA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  31   14  0.58
  32   10  0.42

ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32


Consensus pattern (31 bp):   
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG

Found at i:9369 original size:26 final size:27

Alignment explanation


    Indices: 9316--9369  Score: 74
    Period size: 29  Copynumber: 2.0  Consensus size: 27

       9306 GATTCCAATT

                                         
       9316 AAGGGTCAAATTGATGGCCAAAAGTAATG
          1 AAGGGTCAAATTGA--GCCAAAAGTAATG

                                 *    
       9345 AAGGGTCAAATTGA-CCAAAATTAAT
          1 AAGGGTCAAATTGAGCCAAAAGTAAT

       9370 CGAATAAGGG


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  26   10  0.42
  29   14  0.58

ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22


Consensus pattern (27 bp):   
AAGGGTCAAATTGAGCCAAAAGTAATG
Done.