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FSplice |
Program provides the possibility to search for both donor and acceptor sites, and to define thresholds for them independently. Program allows to search minor variants of splicing donor site (GC-site) as well.
Output example
FSplice 1.0. Prediction of potential splice sites in Homo_sapiens genomic DNA
Seq name: NM_000449 chr 1 - 148089557 148094091 4535
Length of sequence: 4535
Direct chain.
Acceptor(AG) sites. Treshold 4.175 (90%).
1 P: 187 W: 7.47 Seq: attctAGccctc
2 P: 296 W: 6.42 Seq: tcttcAGaggct
3 P: 495 W: 7.30 Seq: tccctAGcagtc
4 P: 498 W: 5.72 Seq: ctagcAGtcaga
5 P: 559 W: 14.18 Seq: cccacAGcaagg
6 P: 847 W: 6.42 Seq: atggtAGcctat
7 P: 1332 W: 9.70 Seq: acctcAGcaaga
8 P: 1383 W: 9.25 Seq: ccttcAGctccc
9 P: 1393 W: 5.38 Seq: ccctcAGgaccc
10 P: 1673 W: 9.95 Seq: tctgtAGctcag
11 P: 1721 W: 4.72 Seq: cctatAGgtgga
12 P: 1916 W: 6.72 Seq: tccctAGggact
13 P: 1984 W: 9.70 Seq: cactcAGgaagt
14 P: 2366 W: 12.18 Seq: ctcccAGgtaaa
15 P: 2467 W: 7.12 Seq: cctgtAGctgag
16 P: 2638 W: 7.42 Seq: acttcAGccaga
17 P: 2779 W: 6.42 Seq: gctacAGcagca
18 P: 2867 W: 6.42 Seq: gtctcAGcaacc
19 P: 2995 W: 5.03 Seq: ctaccAGtcagt
20 P: 3033 W: 5.85 Seq: tcctcAGtttcc
21 P: 3078 W: 9.68 Seq: tctgcAGaagag
22 P: 3342 W: 9.88 Seq: tttttAGcctcc
23 P: 3545 W: 8.12 Seq: cccccAGgcttt
24 P: 4435 W: 6.70 Seq: tcctaAGgaagt
25 P: 4458 W: 6.65 Seq: tgtacAGacagc
26 P: 4513 W: 5.65 Seq: ttttcAGcttga
27 P: 4533 W: 4.58 Seq: gctttAGtg---
Donor(GT) sites. Treshold 6.099 (90%).
1 P: 40 W: 8.20 Seq: aagtgGTgagaa
2 P: 150 W: 7.50 Seq: ccagtGTgagtt
3 P: 307 W: 7.64 Seq: ccgagGTaccat
4 P: 317 W: 9.32 Seq: atttcGTaagta
5 P: 594 W: 15.48 Seq: tcctgGTaagtg
6 P: 691 W: 9.60 Seq: gagagGTagggt
7 P: 1416 W: 13.38 Seq: aaaagGTaggtt
8 P: 1794 W: 7.36 Seq: tatcgGTgggtg
9 P: 2325 W: 10.44 Seq: agagtGTaagta
10 P: 2367 W: 13.10 Seq: cccagGTaaaag
11 P: 2438 W: 8.06 Seq: tctagGTatgat
12 P: 2841 W: 7.36 Seq: cgctgGTgtgtt
13 P: 3180 W: 14.08 Seq: cccagGTaagga
14 P: 3733 W: 10.16 Seq: gagagGTaggca
15 P: 3796 W: 8.62 Seq: tacctGTgagtg
16 P: 4177 W: 11.56 Seq: caaaaGTgagtg
17 P: 4237 W: 6.38 Seq: gagagGTagaca
18 P: 4341 W: 8.06 Seq: tacagGTctgtg
Reverse chain.
Acceptor(AG) sites. Treshold 4.175 (90%).
1 P: 193 W: 6.42 Seq: cccacAGacctg
2 P: 292 W: 5.40 Seq: ggtgcAGtgtct
3 P: 316 W: 4.58 Seq: gccaaAGgaaaa
4 P: 481 W: 8.07 Seq: ttttcAGcctct
5 P: 517 W: 10.38 Seq: cctccAGctgag
6 P: 646 W: 4.17 Seq: tttcgAGggcgc
7 P: 709 W: 7.05 Seq: gctttAGctggt
8 P: 742 W: 6.70 Seq: ctcacAGgtact
9 P: 1424 W: 5.67 Seq: ggtttAGatgac
10 P: 1463 W: 6.97 Seq: tctgcAGaggta
11 P: 1964 W: 7.45 Seq: ttgtcAGagatc
12 P: 2035 W: 6.78 Seq: attgcAGaagcc
13 P: 2068 W: 7.25 Seq: gcctcAGctaca
14 P: 2287 W: 4.72 Seq: actgtAGcaata
15 P: 2397 W: 9.20 Seq: ctcccAGgtcct
16 P: 2421 W: 4.40 Seq: tctctAGtcaag
17 P: 2748 W: 5.08 Seq: ccgatAGgcatc
18 P: 2798 W: 5.47 Seq: cttccAGgtggt
19 P: 3064 W: 6.58 Seq: ttcccAGtgaac
20 P: 3133 W: 10.05 Seq: tctccAGtggtg
21 P: 3901 W: 9.50 Seq: ccctcAGcattt
22 P: 3945 W: 6.03 Seq: ttaccAGgatcc
23 P: 4298 W: 4.72 Seq: cccccAGtcttg
24 P: 4406 W: 11.57 Seq: tccccAGaaggc
25 P: 4440 W: 9.12 Seq: tacccAGaaagg
Donor(GT) sites. Treshold 6.099 (90%).
1 P: 31 W: 8.48 Seq: aaaagGTcagag
2 P: 49 W: 10.02 Seq: accagGTactaa
3 P: 400 W: 7.08 Seq: ctttgGTatgct
4 P: 743 W: 10.02 Seq: cacagGTacttc
5 P: 832 W: 6.80 Seq: gctgaGTgagtc
6 P: 896 W: 12.40 Seq: agttgGTaagat
7 P: 1218 W: 7.64 Seq: acacaGTaaggt
8 P: 1223 W: 8.90 Seq: gtaagGTgtgaa
9 P: 1466 W: 7.64 Seq: cagagGTaccaa
10 P: 1477 W: 12.26 Seq: aaaagGTaatag
11 P: 1491 W: 11.84 Seq: tgaagGTgagga
12 P: 1830 W: 7.64 Seq: cacagGTcaggg
13 P: 2196 W: 6.94 Seq: ggaagGTgattt
14 P: 2686 W: 6.80 Seq: catggGTgaggg
15 P: 2982 W: 7.22 Seq: ccctgGTaaacc
16 P: 3159 W: 9.32 Seq: tgaagGTagaga
17 P: 3209 W: 10.16 Seq: ctgagGTaggag
18 P: 3773 W: 6.80 Seq: atcaaGTgagag
19 P: 4253 W: 8.34 Seq: gggtgGTaggtt
Acceptor(AG) sites. - the type of splicing sites. For the current case "Acceptor(AG)" means the U2-type acceptor site. Possible variants: Donor(GT) sites. means U2-type donor GT-site (Major variant). Donor(GC) sites. means U2-type donor GC- site (Minor variant).
Treshold 4.175 (90%) - means that for the current threshold value (4.175) 90% of true splicing sites are being classified as true.
P: 187 - position of splicing site
W: - weight of site.