Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022686.1 Corchorus olitorius cultivar O-4 contig22719, 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: 8659
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32


Found at i:60 original size:12 final size:12

Alignment explanation


    Indices: 43--67  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

         33 GGGTGGCGGC

                        
         43 ACTAGAAGAAAA
          1 ACTAGAAGAAAA

                        
         55 ACTAGAAGAAAA
          1 ACTAGAAGAAAA

             
         67 A
          1 A

         68 GATCTAAAAC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08


Consensus pattern (12 bp):   
ACTAGAAGAAAA

Found at i:3404 original size:10 final size:10

Alignment explanation


    Indices: 3389--3418  Score: 60
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       3379 AAGCAATACT

                      
       3389 TCCCCACTTA
          1 TCCCCACTTA

                      
       3399 TCCCCACTTA
          1 TCCCCACTTA

                      
       3409 TCCCCACTTA
          1 TCCCCACTTA

       3419 AGTAACAAGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.20, C:0.50, G:0.00, T:0.30


Consensus pattern (10 bp):   
TCCCCACTTA

Found at i:6469 original size:41 final size:40

Alignment explanation


    Indices: 6365--6513  Score: 151
    Period size: 41  Copynumber: 3.7  Consensus size: 40

       6355 GTAATTCAAG

                                       *         ** 
       6365 GTGACAACTTCTGGTGTCAC--TAATTATAATTTACTGGA
          1 GTGACAACTTCTGGTGTCACAGTAATTTTAATTTACTAAA

              *       *  *     *                 *   
       6403 GTCAC-ACTTTTGATGTCAAAGGTAATTTTAATTTACCAAA
          1 GTGACAACTTCTGGTGTCACA-GTAATTTTAATTTACTAAA

                      *                   *          
       6443 GTGACAACTTTTGGTGTCAGCAGTAATTTTGATTTACTAAA
          1 GTGACAACTTCTGGTGTCA-CAGTAATTTTAATTTACTAAA

                               *          
       6484 GTGACAACTTCTGGTGTCAAAGGTAATTTT
          1 GTGACAACTTCTGGTGTCACA-GTAATTTT

       6514 CAATATTATA


Statistics
Matches: 90,  Mismatches: 15, Indels: 9
        0.79            0.13        0.08

Matches are distributed among these distances:
  37   11  0.12
  38    4  0.04
  40   19  0.21
  41   55  0.61
  42    1  0.01

ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38


Consensus pattern (40 bp):   
GTGACAACTTCTGGTGTCACAGTAATTTTAATTTACTAAA
Done.