Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005966.1 Corchorus olitorius cultivar O-4 contig05991, 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, 870

Length: 1450
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28


Found at i:126 original size:49 final size:49

Alignment explanation


    Indices: 49--175  Score: 168
    Period size: 49  Copynumber: 2.6  Consensus size: 49

         39 GAGCGTGCCA

                         *         *                   *      
         49 ATCAATTTTGTCAAAAAAATTGATAAAAAAATGCAA-TGAAAATTAAAAG
          1 ATCAATTTTGTCATAAAAATTGAGAAAAAAATGCAAGT-AAAAATAAAAG

                        *                *                   
         98 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTCATAAAAATTGAGAAAAAAATGCAAGTAAAAATAAAAG

            *                             
        147 TTCAATTTTGT-AGTAAAAATTGAGAAAAA
          1 ATCAATTTTGTCA-TAAAAATTGAGAAAAA

        176 GTGCAGAAAA


Statistics
Matches: 69,  Mismatches: 7, Indels: 4
        0.86            0.09        0.05

Matches are distributed among these distances:
  49   68  0.99
  50    1  0.01

ACGTcount: A:0.54, C:0.06, G:0.13, T:0.28


Consensus pattern (49 bp):   
ATCAATTTTGTCATAAAAATTGAGAAAAAAATGCAAGTAAAAATAAAAG

Found at i:176 original size:49 final size:48

Alignment explanation


    Indices: 49--194  Score: 165
    Period size: 49  Copynumber: 3.0  Consensus size: 48

         39 GAGCGTGCCA

                         *         *     *             *      
         49 ATCAATTTTGTCAAAAAAATTGATAAAAAAATGCAA-TGAAAATTAAAAG
          1 ATCAATTTTGT-ATAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAG

                        *                                    
         98 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGT-ATAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG

            *                                         *      
        147 TTCAATTTTGTAGTAAAAATTGAGAAAAAG-TGC-AG-AAAAGTAAAAG
          1 ATCAATTTTGTA-TAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG

              
        193 AT
          1 AT

        195 TGCTTTAAGT


Statistics
Matches: 86,  Mismatches: 9, Indels: 7
        0.84            0.09        0.07

Matches are distributed among these distances:
  46   11  0.13
  47    2  0.02
  48    3  0.03
  49   69  0.80
  50    1  0.01

ACGTcount: A:0.53, C:0.05, G:0.14, T:0.27


Consensus pattern (48 bp):   
ATCAATTTTGTATAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
Done.