Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002048.1 Corchorus olitorius cultivar O-4 contig02048, 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, 618

Length: 1030
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30


Found at i:95 original size:21 final size:21

Alignment explanation


    Indices: 71--137  Score: 57
    Period size: 21  Copynumber: 3.2  Consensus size: 21

         61 AATTCTCTGT

                                 
         71 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

                *         *   **  *
         92 AAATCATAGAAA-ATTC-TTTGT
          1 AAATTA-AGAAATACTCAACT-C

                                 
        113 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

                
        134 AAAT
          1 AAAT

        138 CCCGATCCTT


Statistics
Matches: 32,  Mismatches: 10, Indels: 8
        0.64            0.20        0.16

Matches are distributed among these distances:
  20    6  0.19
  21   20  0.62
  22    6  0.19

ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28


Consensus pattern (21 bp):   
AAATTAAGAAATACTCAACTC

Found at i:117 original size:42 final size:42

Alignment explanation


    Indices: 58--138  Score: 153
    Period size: 42  Copynumber: 1.9  Consensus size: 42

         48 GCTAAGTCTT

                                                      
         58 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

                     *                             
        100 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC

        139 CCGATCCTTA


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   38  1.00

ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30


Consensus pattern (42 bp):   
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

Found at i:282 original size:56 final size:56

Alignment explanation


    Indices: 204--317  Score: 201
    Period size: 56  Copynumber: 2.0  Consensus size: 56

        194 TTTATTTTGT

                                                                    
        204 AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA

                            **          *                           
        260 AGAATAATTAAGTAGAGTTAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA

              
        316 AG
          1 AG

        318 GAAACAGATA


Statistics
Matches: 55,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  56   55  1.00

ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34


Consensus pattern (56 bp):   
AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Done.