Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016431.1 Corchorus olitorius cultivar O-4 contig16464, 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: 48799
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:21030 original size:28 final size:27

Alignment explanation


    Indices: 20988--21040  Score: 72
    Period size: 26  Copynumber: 1.9  Consensus size: 27

      20978 ACTGAGACTA

                      *                  
      20988 GACTCGAAACTGACTCGAAAAAACAAATT
          1 GACTCGAAACCGACTC--AAAAACAAATT

                                     
      21017 GACTC-AAACCGACTCAAAAACAAA
          1 GACTCGAAACCGACTCAAAAACAAA

      21041 CTCAAATAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  26    9  0.39
  28    9  0.39
  29    5  0.22

ACGTcount: A:0.51, C:0.25, G:0.11, T:0.13


Consensus pattern (27 bp):   
GACTCGAAACCGACTCAAAAACAAATT

Found at i:21784 original size:18 final size:18

Alignment explanation


    Indices: 21745--21785  Score: 50
    Period size: 17  Copynumber: 2.4  Consensus size: 18

      21735 GACGATGTAT

                           *  
      21745 TATATA-ATTTGCCATTA
          1 TATATATATTTGCCAATA

                       *      
      21762 T-TATATATTTTCCAATA
          1 TATATATATTTGCCAATA

                   
      21779 TATATAT
          1 TATATAT

      21786 CTTAGTTCAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 3
        0.80            0.08        0.12

Matches are distributed among these distances:
  16    4  0.20
  17   11  0.55
  18    5  0.25

ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51


Consensus pattern (18 bp):   
TATATATATTTGCCAATA

Found at i:22908 original size:13 final size:13

Alignment explanation


    Indices: 22890--22916  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      22880 AAACAACTGA

                         
      22890 AAAGCACTTCTGG
          1 AAAGCACTTCTGG

                         
      22903 AAAGCACTTCTGG
          1 AAAGCACTTCTGG

             
      22916 A
          1 A

      22917 TTTTCCGTTT


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

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22


Consensus pattern (13 bp):   
AAAGCACTTCTGG
Done.