Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006450.1 Corchorus capsularis cultivar CVL-1 contig06471, 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: 8595
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32


Found at i:3368 original size:19 final size:19

Alignment explanation


    Indices: 3346--3385  Score: 55
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       3336 TGCAATGGGG

                      *         
       3346 AAGAATGAAACAG-AAAGGA
          1 AAGAA-GAAAAAGAAAAGGA

                               
       3365 AAGAAGAAAAAGAAAAGGA
          1 AAGAAGAAAAAGAAAAGGA

              
       3384 AA
          1 AA

       3386 CCAAAAGAGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  18    6  0.32
  19   13  0.68

ACGTcount: A:0.70, C:0.03, G:0.25, T:0.03


Consensus pattern (19 bp):   
AAGAAGAAAAAGAAAAGGA

Found at i:8147 original size:20 final size:20

Alignment explanation


    Indices: 8122--8160  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       8112 AAAAAGAGCA

                                
       8122 CCAATTTGCAAATCAAATGT
          1 CCAATTTGCAAATCAAATGT

                    *          
       8142 CCAATTTGTAAATCAAATG
          1 CCAATTTGCAAATCAAATG

       8161 CCTTGTATTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31


Consensus pattern (20 bp):   
CCAATTTGCAAATCAAATGT

Found at i:8254 original size:18 final size:18

Alignment explanation


    Indices: 8217--8254  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       8207 AATGTAAATG

                           *  
       8217 TTTCTTTTCTTTTTTCTT
          1 TTTCTTTTCTTTTTTATT

                               
       8235 TTTCTTTT-TTTTTGTATT
          1 TTTCTTTTCTTTTT-TATT

              
       8253 TT
          1 TT

       8255 GTATTTTCAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  17    5  0.28
  18   13  0.72

ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84


Consensus pattern (18 bp):   
TTTCTTTTCTTTTTTATT
Done.