Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016088.1 Corchorus olitorius cultivar O-4 contig16121, 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: 6725
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32


Found at i:4482 original size:42 final size:43

Alignment explanation


    Indices: 4452--4533  Score: 123
    Period size: 42  Copynumber: 2.0  Consensus size: 43

       4442 TAGAAGGAAG

                             *     *                   
       4452 AGAAGGGGAAGGAGAAGGAGAAGGAGAAGAA-AAGGAAGAATA
          1 AGAAGGGGAAGGAGAAGAAGAAGAAGAAGAAGAAGGAAGAATA

                        *                            
       4494 AGAAGGGGAAGGGGAAGAAGAAGAAGAAGAAG-AGGAAGAA
          1 AGAAGGGGAAGGAGAAGAAGAAGAAGAAGAAGAAGGAAGAA

       4534 ACACTTTTCA


Statistics
Matches: 36,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.55, C:0.00, G:0.44, T:0.01


Consensus pattern (43 bp):   
AGAAGGGGAAGGAGAAGAAGAAGAAGAAGAAGAAGGAAGAATA

Found at i:4523 original size:6 final size:6

Alignment explanation


    Indices: 4436--4533  Score: 56
    Period size: 6  Copynumber: 16.3  Consensus size: 6

       4426 AAAGAGAGGT

                   *                 **     *      *      *         
       4436 AAGAAG TAGAAGG AAG-AG AAGGGG AAGGAG AAGGAG AAGGAG AAGAA-
          1 AAGAAG AAGAA-G AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG

                      *       **     **                        *    
       4483 AAGGAAG AATAAG AAGGGG AAGGGG AAGAAG AAGAAG AAGAAG AGGAAG
          1 AA-GAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG

              
       4532 AA
          1 AA

       4534 ACACTTTTCA


Statistics
Matches: 75,  Mismatches: 13, Indels: 8
        0.78            0.14        0.08

Matches are distributed among these distances:
   5    6  0.08
   6   64  0.85
   7    5  0.07

ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02


Consensus pattern (6 bp):   
AAGAAG

Found at i:4531 original size:15 final size:15

Alignment explanation


    Indices: 4417--4533  Score: 52
    Period size: 15  Copynumber: 8.0  Consensus size: 15

       4407 TTGGGATTGG

                     *      
       4417 GAAGAAGAGAAAGAGA
          1 GAAGAAGAGGAAGA-A

                               
       4433 GGTAAGAAGTA-GAAGGAA
          1 -G-AAGAAG-AGGAA-GAA

                   *     * 
       4451 G-AGAAGGGGAAGGA
          1 GAAGAAGAGGAAGAA

                         * 
       4465 GAAG--GA-GAAGGA
          1 GAAGAAGAGGAAGAA

                  *        
       4477 GAAGAAAAGGAAGAA
          1 GAAGAAGAGGAAGAA

            *              
       4492 TAAGAAG-GG--GAA
          1 GAAGAAGAGGAAGAA

             **     *      
       4504 GGGGAAGAAGAAGAA
          1 GAAGAAGAGGAAGAA

                           
       4519 GAAGAAGAGGAAGAA
          1 GAAGAAGAGGAAGAA

       4534 ACACTTTTCA


Statistics
Matches: 74,  Mismatches: 15, Indels: 24
        0.65            0.13        0.21

Matches are distributed among these distances:
  12   17  0.23
  13    2  0.03
  14    6  0.08
  15   35  0.47
  17    2  0.03
  18    9  0.12
  19    3  0.04

ACGTcount: A:0.55, C:0.00, G:0.43, T:0.03


Consensus pattern (15 bp):   
GAAGAAGAGGAAGAA

Found at i:5945 original size:3 final size:3

Alignment explanation


    Indices: 5939--5967  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       5929 TTTTCCACAT

                                                   
       5939 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

       5968 CATATATAAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.08
   3   23  0.92

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TTA

Found at i:5959 original size:14 final size:14

Alignment explanation


    Indices: 5940--5967  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       5930 TTTCCACATT

                          
       5940 TATTATTATTATTA
          1 TATTATTATTATTA

                          
       5954 TATTATTATTATTA
          1 TATTATTATTATTA

       5968 CATATATAAG


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

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (14 bp):   
TATTATTATTATTA
Done.