Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013410.1 Corchorus olitorius cultivar O-4 contig13443, 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: 22320
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:12444 original size:18 final size:18

Alignment explanation


    Indices: 12398--12462  Score: 76
    Period size: 18  Copynumber: 3.6  Consensus size: 18

      12388 GGTTCTTGCG

                *             
      12398 GCAGCGGAACATCCTGCA
          1 GCAGTGGAACATCCTGCA

               *  *     *     
      12416 GCAATGTAACATTCTGCA
          1 GCAGTGGAACATCCTGCA

             *               *
      12434 GTAGTGGAACATCCTGCG
          1 GCAGTGGAACATCCTGCA

                       
      12452 GCAGTGGAACA
          1 GCAGTGGAACA

      12463 ATATTTTGTA


Statistics
Matches: 37,  Mismatches: 10, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   37  1.00

ACGTcount: A:0.29, C:0.25, G:0.28, T:0.18


Consensus pattern (18 bp):   
GCAGTGGAACATCCTGCA

Found at i:15017 original size:17 final size:17

Alignment explanation


    Indices: 14995--15030  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      14985 ATACATAGAG

                   *         
      14995 CTATCTAGTATAACAAA
          1 CTATCTAATATAACAAA

                     *       
      15012 CTATCTAATGTAACAAA
          1 CTATCTAATATAACAAA

              
      15029 CT
          1 CT

      15031 TTACAAATCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31


Consensus pattern (17 bp):   
CTATCTAATATAACAAA

Found at i:22285 original size:25 final size:26

Alignment explanation


    Indices: 22257--22305  Score: 73
    Period size: 26  Copynumber: 1.9  Consensus size: 26

      22247 AATACTTACA

                         *    *       
      22257 TTAATT-AAATTCTTAGGTATTTTTT
          1 TTAATTCAAATTCGTAGGCATTTTTT

                                    
      22282 TTAATTCAAATTCGTAGGCATTTT
          1 TTAATTCAAATTCGTAGGCATTTT

      22306 GTGCAAACGT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25    6  0.29
  26   15  0.71

ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53


Consensus pattern (26 bp):   
TTAATTCAAATTCGTAGGCATTTTTT

Done.