In the below example, we want to search the DNA sequence ACGTCGTAACGTCATCGT for all tandem repeats with the basic unit: CGT.
In the form, we enter the basic unit in the Pattern To Search On field, and the sequence in the Text Sequence field. Now, we enter the length of the DNA sequence in the Text Length field. Next, check the interactive results button to generate a page interactively and display it. The radio button for email results allows the choice of HTML, text, or a URL (pointing to a temporary location online).
The scoring options may be defined as follows: For explanition of how scoring matrix is used, click here.
Upon pressing submit, the algorithm will generate the following output, where the first collumn represents the start of the tandem repeat region, and the second collumn represents the end. A score of 1000000 is perfect, score of 0 indicates that this region is incompatible. This output is in a format which may be used by GNUplot.
Note: in the example DNA sequence- ACGTCGTAACGTCATCGT, window position 1 corresponds to "A", with window position 2 corresponding to "C", and ending with window position 18 corresponding to "T"
Text length is 19.
Patt length is 3.
1 1 0
1 2 500000
1 3 666666
1 4 750000
1 5 800000
1 6 833333
1 7 857142
1 8 750000
1 9 666666
1 10 600000
1 11 545454
1 12 500000
1 13 461538
1 14 428571
1 15 400000
1 16 375000
1 17 411764
1 18 444444
2 2 1000000
2 3 1000000
2 4 1000000
2 5 1000000
2 6 1000000
2 7 1000000
2 8 857142
2 9 750000
2 10 666666
2 11 600000
2 12 545454
2 13 500000
2 14 461538
2 15 428571
2 16 400000
2 17 437500
2 18 470588
3 3 1000000
3 4 1000000
3 5 1000000
3 6 1000000
3 7 1000000
3 8 833333
3 9 714285
3 10 625000
3 11 555555
3 12 500000
3 13 454545
3 14 416666
3 15 384615
3 16 357142
3 17 400000
3 18 437500
4 4 1000000
4 5 1000000
4 6 1000000
4 7 1000000
4 8 800000
4 9 666666
4 10 571428
4 11 500000
4 12 444444
4 13 400000
4 14 363636
4 15 333333
4 16 384615
4 17 428571
4 18 466666
5 5 1000000
5 6 1000000
5 7 1000000
5 8 750000
5 9 600000
5 10 500000
5 11 428571
5 12 375000
5 13 444444
5 14 400000
5 15 363636
5 16 416666
5 17 461538
5 18 500000
6 6 1000000
6 7 1000000
6 8 666666
6 9 500000
6 10 400000
6 11 333333
6 12 428571
6 13 500000
6 14 444444
6 15 400000
6 16 454545
6 17 500000
6 18 538461
7 7 1000000
7 8 500000
7 9 333333
7 10 250000
7 11 400000
7 12 500000
7 13 571428
7 14 500000
7 15 444444
7 16 500000
7 17 545454
7 18 583333
8 8 0
8 9 0
8 10 333333
8 11 500000
8 12 600000
8 13 666666
8 14 571428
8 15 500000
8 16 555555
8 17 600000
8 18 636363
9 9 0
9 10 500000
9 11 666666
9 12 750000
9 13 800000
9 14 666666
9 15 571428
9 16 625000
9 17 666666
9 18 700000
10 10 1000000
10 11 1000000
10 12 1000000
10 13 1000000
10 14 800000
10 15 666666
10 16 714285
10 17 750000
10 18 777777
11 11 1000000
11 12 1000000
11 13 1000000
11 14 750000
11 15 600000
11 16 666666
11 17 714285
11 18 750000
12 12 1000000
12 13 1000000
12 14 666666
12 15 500000
12 16 600000
12 17 666666
12 18 714285
13 13 1000000
13 14 500000
13 15 333333
13 16 500000
13 17 600000
13 18 666666
14 14 0
14 15 500000
14 16 666666
14 17 750000
14 18 800000
15 15 1000000
15 16 1000000
15 17 1000000
15 18 1000000
16 16 1000000
16 17 1000000
16 18 1000000
17 17 1000000
17 18 1000000
18 18 1000000
Program finished. Output written to /s/www/scripts/samp.out.
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