Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020670.1 Corchorus olitorius cultivar O-4 contig20703, 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: 6227
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28


Found at i:117 original size:16 final size:16

Alignment explanation


    Indices: 71--124  Score: 58
    Period size: 15  Copynumber: 3.4  Consensus size: 16

         61 GAACCGTATA

                      *    * 
         71 ACCCGAAACCGAAAACG
          1 ACCCG-AACCCAAAATG

                             
         88 ACCC-AACCCAAAATTG
          1 ACCCGAACCCAAAA-TG

                            
        104 ACCCGAACCC-AAATG
          1 ACCCGAACCCAAAATG

                  
        119 ACCCGA
          1 ACCCGA

        125 CATTTGAACG


Statistics
Matches: 33,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  15   16  0.48
  16    8  0.24
  17    9  0.27

ACGTcount: A:0.43, C:0.39, G:0.13, T:0.06


Consensus pattern (16 bp):   
ACCCGAACCCAAAATG

Found at i:1432 original size:25 final size:25

Alignment explanation


    Indices: 1403--1461  Score: 84
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       1393 AAAAGTCGAG

                    *        *        
       1403 AGAAAGGGGGAAGAGGAGAAGAG-AA
          1 AGAAAGGGAGAAG-GGAAAAGAGAAA

                                     
       1428 AGAAAGGGAGAAGGGAAAAGAGAAA
          1 AGAAAGGGAGAAGGGAAAAGAGAAA

                     
       1453 AGAAAGGGA
          1 AGAAAGGGA

       1462 ACAATATGGA


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  24    8  0.26
  25   23  0.74

ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00


Consensus pattern (25 bp):   
AGAAAGGGAGAAGGGAAAAGAGAAA
Done.