Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020737.1 Corchorus olitorius cultivar O-4 contig20770, 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: 5486
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:698 original size:6 final size:6

Alignment explanation


    Indices: 687--738  Score: 54
    Period size: 6  Copynumber: 8.5  Consensus size: 6

        677 TTGACAGCGC

                             *                                        
        687 AACAAA AAC-AA AACGAA AAC-AA AACAAA AACAAAA AACAGAAA AACAAA
          1 AACAAA AACAAA AACAAA AACAAA AACAAA AAC-AAA AAC--AAA AACAAA

               
        736 AAC
          1 AAC

        739 GATACCAAAC


Statistics
Matches: 41,  Mismatches: 1, Indels: 8
        0.82            0.02        0.16

Matches are distributed among these distances:
   5   10  0.24
   6   19  0.46
   7    6  0.15
   8    6  0.15

ACGTcount: A:0.79, C:0.17, G:0.04, T:0.00


Consensus pattern (6 bp):   
AACAAA

Found at i:707 original size:11 final size:11

Alignment explanation


    Indices: 687--738  Score: 63
    Period size: 11  Copynumber: 4.8  Consensus size: 11

        677 TTGACAGCGC

                       
        687 AACAAAAACAA
          1 AACAAAAACAA

               *       
        698 AACGAAAACAA
          1 AACAAAAACAA

                       
        709 AACAAAAACAA
          1 AACAAAAACAA

                   *    
        720 AA-AACAGA-AA
          1 AACAA-AAACAA

                     
        730 AACAAAAAC
          1 AACAAAAAC

        739 GATACCAAAC


Statistics
Matches: 34,  Mismatches: 4, Indels: 6
        0.77            0.09        0.14

Matches are distributed among these distances:
  10    8  0.24
  11   26  0.76

ACGTcount: A:0.79, C:0.17, G:0.04, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA
Done.