Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018558.1 Corchorus olitorius cultivar O-4 contig18591, 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: 16729
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31


Found at i:2953 original size:16 final size:16

Alignment explanation


    Indices: 2932--2972  Score: 64
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       2922 GCCATAAAAG

                            
       2932 CCCGGCCCGAGCCCGA
          1 CCCGGCCCGAGCCCGA

                           *
       2948 CCCGGCCCGAGCCCGG
          1 CCCGGCCCGAGCCCGA

            *        
       2964 TCCGGCCCG
          1 CCCGGCCCG

       2973 TATGCTTAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  16   23  1.00

ACGTcount: A:0.07, C:0.56, G:0.34, T:0.02


Consensus pattern (16 bp):   
CCCGGCCCGAGCCCGA

Found at i:3336 original size:11 final size:11

Alignment explanation


    Indices: 3320--3359  Score: 64
    Period size: 11  Copynumber: 3.7  Consensus size: 11

       3310 AAAGCTTGGG

                       
       3320 CCCGGCCCGAA
          1 CCCGGCCCGAA

                       
       3331 CCCGGCCCGAA
          1 CCCGGCCCGAA

                      *
       3342 CCCGGCCC-AG
          1 CCCGGCCCGAA

                    
       3352 CCCGGCCC
          1 CCCGGCCC

       3360 ATGAACACCT


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  10    9  0.32
  11   19  0.68

ACGTcount: A:0.12, C:0.60, G:0.28, T:0.00


Consensus pattern (11 bp):   
CCCGGCCCGAA

Found at i:15493 original size:21 final size:21

Alignment explanation


    Indices: 15450--15493  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      15440 CCAATTTAGG

                   *       *     
      15450 TTTAGATTTAAATTTCTTGTT
          1 TTTAGATCTAAATTTATTGTT

                                  
      15471 TTTAGATCTAAGATTTATT-TT
          1 TTTAGATCTAA-ATTTATTGTT

              
      15492 TT
          1 TT

      15494 ATGCATCTTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21   14  0.70
  22    6  0.30

ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61


Consensus pattern (21 bp):   
TTTAGATCTAAATTTATTGTT
Done.