NetGene2 World Wide Web Server

Center for Biological Sequence Analysis

The Technical University of Denmark

DK-2800 Lyngby, Denmark

Performing prediction for D_gene (size: 4350) Species: A. thaliana

Starting prediction in + strand

Starting prediction in - strand

Preparing output

Prediction done

********************** NetGene2 v. 2.4 ************************ The sequence: D_gene has the following composition: Length: 4350 nucleotides. 28.7% A, 23.0% C, 18.6% G, 29.7% T, 0.0% X, 41.6% G+C Donor splice sites, direct strand --------------------------------- pos 5'->3' phase strand confidence 5' exon intron 3' 174 0 + 0.88 ACCCCACTAC^GTAAAAATAA 2280 1 + 1.00 GCTCTTTCAA^GTGAGTTAAT H 2572 1 + 1.00 CTTCTTGAAG^GTAAACTATG H 2998 0 + 1.00 GACTCTTGAG^GTATATATTA H 3308 1 + 0.88 CGTCTCTCAG^GTAACAATAC 3914 1 + 1.00 GTTTCTTAAG^GTGAGATCTC Donor splice sites, complement strand ------------------------------------- pos 3'->5' pos 5'->3' phase strand confidence 5' exon intron 3' 4228 123 1 - 0.87 GGTACTGGAG^GTAGTGATTT 4189 162 1 - 0.96 GCAACGAAGG^GTAAGTAAGT H 2724 1627 0 - 0.74 GAACATCAAT^GTAACCAAGA Acceptor splice sites, direct strand ------------------------------------ pos 5'->3' phase strand confidence 5' intron exon 3' 991 1 + 0.76 CTTTACTTAG^GAACAATGGT 1971 0 + 0.65 AATTTTACAG^TCTCGTGTGC 2365 2 + 0.94 TGGTTTGCAG^ATTAGATGAG 2752 1 + 0.88 GCTTTTTCAG^GCAATGCTGA 3081 0 + 1.00 GTTTGTGTAG^GCTGCTTGTG H Acceptor splice sites, complement strand ---------------------------------------- pos 3'->5' pos 5'->3' phase strand confidence 5' intron exon 3' 2484 1867 1 - 0.71 TCGGGTCCAG^GACTCTGTTC 261 4090 2 - 0.94 CTTAACTCAG^TGATGGTGAG Branch points, direct strand ---------------------------- acceptor branch pos 5'->3' pos 5'->3' strand score 5' A 3' 991 976 + -3.84 AACAGCTCTGAGTTTCTTTA 1971 1960 + -2.01 ATTTCACCTCAAATTTTACA 2365 2351 + -2.09 TGAGATTATGAATGTGGTTT 2752 2736 + -2.02 TGATGTTCTTAGTTATGCTT 3081 3051 + -2.27 ATTGTAACAGATTATGACTT Branch points, complement strand -------------------------------- acceptor branch pos 5'->3' pos 5'->3' strand score 5' A 3' 2483 2501 - -3.91 CAATATTCTGAGCCTTCTTC 260 316 - -2.37 AATCCAGCTAAGATTCTGCT ------------------------------------------------------------------------------ CUTOFF values used for confidence: Highly confident donor sites (H): 95.0 % Nearly all true donor sites: 50.0 % Highly confident acceptor sites (H): 95.0 % Nearly all true acceptor sites: 20.0 % 

Graphics showing the prediction output

Direct strand ( + strand)








 
 

Complement strand ( - strand)







Graphics in postscript format

Direct Strand 27441 bytes.
Complement Strand 28398 bytes.

Prediction scores files

Direct Strand 42698 bytes.
Complement Strand 42975 bytes.