Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016889.1 Corchorus olitorius cultivar O-4 contig16922, 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: 10701
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36


Found at i:8401 original size:20 final size:20

Alignment explanation


    Indices: 8376--8424  Score: 89
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       8366 GCGTGAATAT

                                
       8376 AGGCCACGTGGAATTATCAG
          1 AGGCCACGTGGAATTATCAG

                                
       8396 AGGCCACGTGGAATTATCAG
          1 AGGCCACGTGGAATTATCAG

               *     
       8416 AGGACACGT
          1 AGGCCACGT

       8425 CATAAAGTCC


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  20   28  1.00

ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18


Consensus pattern (20 bp):   
AGGCCACGTGGAATTATCAG

Found at i:9923 original size:15 final size:15

Alignment explanation


    Indices: 9903--9931  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       9893 GCCCACTGTG

                           
       9903 ACCACTGATAATGTC
          1 ACCACTGATAATGTC

                          
       9918 ACCACTGATAATGT
          1 ACCACTGATAATGT

       9932 TTTTGATGTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28


Consensus pattern (15 bp):   
ACCACTGATAATGTC

Found at i:10214 original size:45 final size:45

Alignment explanation


    Indices: 10141--10309  Score: 248
    Period size: 45  Copynumber: 3.8  Consensus size: 45

      10131 TGCTGCAGAA

                              **** *                     
      10141 GGTGAAAATGTGGATGGGGAACAAGGAGTTAGAGAGGAGAATGAG
          1 GGTGAAAATGTGGATGGGTTTGATGGAGTTAGAGAGGAGAATGAG

                                                         
      10186 GGTGAAAATGTGGATGGGTTTGATGGAGTTAGAGAGGAGAATGAG
          1 GGTGAAAATGTGGATGGGTTTGATGGAGTTAGAGAGGAGAATGAG

             *                      *                    
      10231 GATGAAAATGTGGATGGGTTTGATAGAGTTAGAGAGGAGAATGAG
          1 GGTGAAAATGTGGATGGGTTTGATGGAGTTAGAGAGGAGAATGAG

                     * *           *          
      10276 GGTGAAAATCTTGATGGGTTTGAGGGAGTTAGAG
          1 GGTGAAAATGTGGATGGGTTTGATGGAGTTAGAG

      10310 CCAATAATGG


Statistics
Matches: 112,  Mismatches: 12, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  45  112  1.00

ACGTcount: A:0.33, C:0.01, G:0.43, T:0.23


Consensus pattern (45 bp):   
GGTGAAAATGTGGATGGGTTTGATGGAGTTAGAGAGGAGAATGAG

Found at i:10324 original size:45 final size:45

Alignment explanation


    Indices: 10165--10335  Score: 243
    Period size: 45  Copynumber: 3.8  Consensus size: 45

      10155 TGGGGAACAA

                                          *              
      10165 GGAGTTAGAGAGGAGAATGAGGGTGAAAATGTGGATGGGTTTGAT
          1 GGAGTTAGAGAGGAGAATGAGGGTGAAAATCTGGATGGGTTTGAT

                                  *       *              
      10210 GGAGTTAGAGAGGAGAATGAGGATGAAAATGTGGATGGGTTTGAT
          1 GGAGTTAGAGAGGAGAATGAGGGTGAAAATCTGGATGGGTTTGAT

            *                               *           *
      10255 AGAGTTAGAGAGGAGAATGAGGGTGAAAATCTTGATGGGTTTGAG
          1 GGAGTTAGAGAGGAGAATGAGGGTGAAAATCTGGATGGGTTTGAT

                      *** *    *                
      10300 GGAGTTAGAGCCAATAATGGGGGTGAAAATCTGGAT
          1 GGAGTTAGAGAGGAGAATGAGGGTGAAAATCTGGAT

      10336 AGGTATAACA


Statistics
Matches: 113,  Mismatches: 13, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  45  113  1.00

ACGTcount: A:0.33, C:0.02, G:0.41, T:0.24


Consensus pattern (45 bp):   
GGAGTTAGAGAGGAGAATGAGGGTGAAAATCTGGATGGGTTTGAT

Done.