Also, try to have a look on this page to find a suitable terminator database for you
http://molbiol-tools.ca/Promoters.htm
B. Eukaryotic
Not being a eukaryotic molecular biologist I cannot comment on utility and accuracy of the following promoter- prediction programs.
EPDnew (Eukaryotic Promoter Database) - is a new collection of experimentally validated promoters in human, mouse, D. melanogaster and zebrafish genomes. Evidence comes from TSS-mapping from high-throughput expreriments such as CAGE and Oligocapping. ChIP-seq experiments on H2AZ, H3K4me3, Pol-II and DNA methylation are also taken into account during the analysis. Include promoter analysis tools. (Reference: Dreos, R. et al. 2015. Nucl. Acids Res. 43 (D1):D92-D96).
Promoter 2.0 Prediction Server (S. Knudsen,Center for Biological Sequence Analysis, Technical University of Denmark) - predicts transcription start sites of vertebrate Pol II promoters in DNA sequences
PROMOSER - Human, Mouse and Rat promoter extraction service (Boston University, U.S.A.) - maps promoter sequences and transcription start sites in mammalian genomes. (Reference: S. Anason et al. 2003. Nucl. Acids. Res. 2003 31: 3554-59).
Promoter and gene expression regulatory motifs search (Softberry, U.S.A.) - offers a variety of promoter-scanning programs
GPMiner - identifies promoter regions and annotates regulatory features in user-input sequences. The proposed promoter identification method, whose predictive sensitivity and specificity are both ~80%, incorporates the support vector machine (SVM) with nucleotide composition, over-represented hexamer nucleotides and DNA stability. Additionally, the input sequence also can be analyzed for homogeneity of experimental mammalian promoter sequences. After identifying the promoter regions, the regulatory features such as transcription factor binding sites, CpG islands, tandem repeats, the TATA box, the CCAAT box, the GC box, over-represented oligonucleotides, DNA stability and GC-content are graphically visualized to facilitate the observation of gene promoters.
C. Transcriptional terminators
TransTermHP (A. Villegas, Public Health Ontario, Canada) - an online version of TranstermHP, Reference: Kingsford, C. et al. 2007. Genome Biol. 8: R22) an updated version of TransTerm (Reference: Ermolaeva, M.D. et al. 2000. J Mol Biol301:27-33)
WebGeSTer - Genome Scanner for Terminators - my favourite terminator search program is finally web enabled. Please note that if you want to analyze data from a *.gbk file you need to use their conversion program "GenBank2GeSTer" first. A complete description of each terminator including a diagram is produced by this program. This site linked to an extensive database of transcriptional terminators in bacterial genome (WebGeSTer DB) (Reference: Mitra A. et al. 2011. Nucl. Acids Res. 39(Database issue):D129-35).
ARNold - finds rho-independent terminators in nucleic acid sequences using two complementary programs, Erpin and RNAmotif. The program colors the terminator stem and loop (References: Gautheret D, Lambert A. 2001. J Mol Biol. 313:1003–11 & Macke T. et al. 2001. Nucleic Acids Res. 29:4724–4735 ).
FindTerm (Softberry Inc.) - can also be used for mapping rho-independent terminators. You might consider using the advanced feature options and minimally increase the default energy threshold to -12.0. Please note that the online version of this program will only find one terminator at a time. If you are dealing with a long sequence, once you have located a terminator, delete it from the DNA sequence and resubmit.