Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004727.1 Corchorus capsularis cultivar CVL-1 contig04743, 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, 639

Length: 1065
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28


Found at i:40 original size:27 final size:27

Alignment explanation


    Indices: 1--238  Score: 323
    Period size: 27  Copynumber: 8.3  Consensus size: 27

                                        
          1 GATTCCGGAGGATGAGCTTCAAGAGAAT
          1 GATT-CGGAGGATGAGCTTCAAGAGAAT

                                   *   *     
         29 GATTCGGAGGATGCAGCTTCAGCGGATCATTAT
          1 GATTCGGAGGATG-AGCTTCA--AGA-GA--AT

                                       
         62 GATTCGGAGGATGAGCTTCAAGAGAAT
          1 GATTCGGAGGATGAGCTTCAAGAGAAT

                                       
         89 GATTCGGAGGATGAGCTTCAAGAGAAT
          1 GATTCGGAGGATGAGCTTCAAGAGAAT

                                  *   *      
        116 GATTCGGAGGATGAGCTTCAGCGGATCATTTAT
          1 GATTCGGAGGATGAGCTTCA--AGA-GA---AT

                                       
        149 GATTCGGAGGATGAGCTTCAAGAGAAT
          1 GATTCGGAGGATGAGCTTCAAGAGAAT

                                       
        176 GATTCGGAGGATGAGCTTCAAGAGAAT
          1 GATTCGGAGGATGAGCTTCAAGAGAAT

                                       
        203 GATTCGGAGGATGAGCTTCAAGAGAAT
          1 GATTCGGAGGATGAGCTTCAAGAGAAT

                     
        230 GATTCGGAG
          1 GATTCGGAG

        239 TTCTTGCAGA


Statistics
Matches: 190,  Mismatches: 8, Indels: 25
        0.85            0.04        0.11

Matches are distributed among these distances:
  27  123  0.65
  28   11  0.06
  29    3  0.02
  30    6  0.03
  31    3  0.02
  32    7  0.04
  33   37  0.19

ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24


Consensus pattern (27 bp):   
GATTCGGAGGATGAGCTTCAAGAGAAT

Found at i:99 original size:60 final size:54

Alignment explanation


    Indices: 1--238  Score: 323
    Period size: 60  Copynumber: 4.2  Consensus size: 54

                                                               *   *     
          1 GATTCCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGCAGCTTCAGCGGATCATTAT
          1 GATT-CGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATG-AGCTTCA--AGA-GA--AT

                                                                  
         62 GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAGAAT
          1 GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAGAAT

                                  *   *                                 
        116 GATTCGGAGGATGAGCTTCAGCGGATCATTTATGATTCGGAGGATGAGCTTCAAGAGAAT
          1 GATTCGGAGGATGAGCTTCA--AGA-GA---ATGATTCGGAGGATGAGCTTCAAGAGAAT

                                                                  
        176 GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAGAAT
          1 GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAGAAT

                     
        230 GATTCGGAG
          1 GATTCGGAG

        239 TTCTTGCAGA


Statistics
Matches: 165,  Mismatches: 6, Indels: 19
        0.87            0.03        0.10

Matches are distributed among these distances:
  54   60  0.36
  56    3  0.02
  57    4  0.02
  58    2  0.01
  59    7  0.04
  60   85  0.52
  61    4  0.02

ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24


Consensus pattern (54 bp):   
GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAAGAGAAT

Found at i:152 original size:87 final size:86

Alignment explanation


    Indices: 1--222  Score: 417
    Period size: 87  Copynumber: 2.5  Consensus size: 86

                                                                             
          1 GATTCCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGCAGCTTCAGCGGATCATTATGATT
          1 GATT-CGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATG-AGCTTCAGCGGATCATTATGATT

                                   
         66 CGGAGGATGAGCTTCAAGAGAAT
         64 CGGAGGATGAGCTTCAAGAGAAT

                                                                             
         89 GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAGCGGATCATTTATGATTC
          1 GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAGCGGATCA-TTATGATTC

                                  
        154 GGAGGATGAGCTTCAAGAGAAT
         65 GGAGGATGAGCTTCAAGAGAAT

                                                           
        176 GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCA
          1 GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCA

        223 AGAGAATGAT


Statistics
Matches: 133,  Mismatches: 0, Indels: 3
        0.98            0.00        0.02

Matches are distributed among these distances:
  86   15  0.11
  87  114  0.86
  88    4  0.03

ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24


Consensus pattern (86 bp):   
GATTCGGAGGATGAGCTTCAAGAGAATGATTCGGAGGATGAGCTTCAGCGGATCATTATGATTCG
GAGGATGAGCTTCAAGAGAAT
Done.