Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016311.1 Corchorus olitorius cultivar O-4 contig16344, 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: 2761
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35


Found at i:968 original size:36 final size:36

Alignment explanation


    Indices: 921--990  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        911 GAGATTTTGG

                         *      *               
        921 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAAGCAAAATCACAAAAAATGTAATA

                                       *      
        957 AGAAATATGATAAGCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAAGCAAAATCACAAAAAATGTAA

        991 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.07, G:0.11, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAAGCAAAATCACAAAAAATGTAATA

Found at i:2355 original size:58 final size:58

Alignment explanation


    Indices: 2248--2362  Score: 169
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       2238 ATAGCATCAT

                      *                                               
       2248 GTCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
          1 GTCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA

                                       *             *   *       *    
       2306 GTCTCGGTCCGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACGTGTCACTTGATA
          1 GTCTCGGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA

       2363 TTTGATTAAT


Statistics
Matches: 51,  Mismatches: 5, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  58   35  0.69
  59   16  0.31

ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33


Consensus pattern (58 bp):   
GTCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
Done.