Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000908.1 Corchorus olitorius cultivar O-4 contig00908, 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: 2123
ACGTcount: A:0.22, C:0.29, G:0.30, T:0.20

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:39 original size:22 final size:22

Alignment explanation


    Indices: 5--85  Score: 92
    Period size: 22  Copynumber: 3.7  Consensus size: 22

          1 ATAA

                  *               
          5 AGGTTAACAAAATTTCATGGGG
          1 AGGTTATCAAAATTTCATGGGG

                    *              
         27 AGGTTATCGAAATTTCA-GAGGG
          1 AGGTTATCAAAATTTCATG-GGG

              *               * * 
         49 AGATTATCAAAATTTCATAGTG
          1 AGGTTATCAAAATTTCATGGGG

            *              
         71 TGGTTATCAAAATTT
          1 AGGTTATCAAAATTT

         86 TATAATATGG


Statistics
Matches: 49,  Mismatches: 8, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  21    1  0.02
  22   48  0.98

ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33


Consensus pattern (22 bp):   
AGGTTATCAAAATTTCATGGGG

Found at i:96 original size:22 final size:22

Alignment explanation


    Indices: 52--96  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

         42 CAGAGGGAGA

                            * *   
         52 TTATCAAAATTTCATAGTGTGG
          1 TTATCAAAATTTCATAATATGG

                        *         
         74 TTATCAAAATTTTATAATATGG
          1 TTATCAAAATTTCATAATATGG

             
         96 T
          1 T

         97 ATTTCACAGG


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44


Consensus pattern (22 bp):   
TTATCAAAATTTCATAATATGG

Found at i:185 original size:46 final size:43

Alignment explanation


    Indices: 135--241  Score: 119
    Period size: 46  Copynumber: 2.4  Consensus size: 43

        125 AATTTTGTGG

                                                           
        135 TAACTAAAATTTCATAATGNGTTTATCCAAAAATTTAT-GGTGAGAT
          1 TAACTAAAATTTCATAATG-GTTT-T-CAAAAATTTATAGG-GAGAT

                         *                  *             
        181 TAACTAAAAATTTGATAGAATGGTTTTCAAAATTTTATAGGGAGAT
          1 TAACT-AAAATTTCAT--AATGGTTTTCAAAAATTTATAGGGAGAT

                            
        227 TAAC-AAAATTTCATA
          1 TAACTAAAATTTCATA

        242 GGCAAGTTAT


Statistics
Matches: 54,  Mismatches: 3, Indels: 12
        0.78            0.04        0.17

Matches are distributed among these distances:
  42    1  0.02
  44    9  0.17
  46   24  0.44
  47   12  0.22
  48    4  0.07
  49    4  0.07

ACGTcount: A:0.42, C:0.07, G:0.13, T:0.36


Consensus pattern (43 bp):   
TAACTAAAATTTCATAATGGTTTTCAAAAATTTATAGGGAGAT
Done.