Origin IGS: gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgttaaaaaaattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaatttttttaacgaaataagcagattttacttgatcgctatatattaaattgtataatgaagctgtttttatttaaggtggtcgtcattcttaaacacagtggccggtgcaaacaactccccc Mask Tandem Repeat Region ================================================ gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgttaaaaaaattta Find is-nt database================================================ Query_seq: AA01739:AA01740|AA01739:AA01740:conserved hypothetical protein:conserved hypothetical protein:->->:1176573..1176697 125 gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgttaaaaaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01739:AA01740|AA01739:AA01740:conserved hypothetical protein:conserved hypothetical protein:->->:1176573..1176697 125 gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgttaaaaaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01739:AA01740|AA01739:AA01740:conserved hypothetical protein:conserved hypothetical protein:->->:1176573..1176697 125 gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgttaaaaaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgttaaaaaaattta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 2 End: 100 . P L Q K C R G S H K L I V V V K F L F L K M I C N L I Y R D L L M ......................... gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgttaaaaaaattta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgttaaaaaaattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01739:AA01740|AA01739:AA01740:conserved hypothetical protein:conserved hypothetical protein:->->:1176573..1176697 125 gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgttaaaaaaattta Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: aact_AA01739_AA01740|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1176573,1176697]|125 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgtt........... gggggagttgtttgcaccggccactgtgtttaagaatgacgaccaccttaaataaaaacagcttcattatacaatttaatatatagcgatcaagtaaaatctgcttatttcgtt........... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGGAGUUGUUUGCACCGGCCACUGUGUUUAAGAAUGACGACCACCUUAAAUAAAAACAGCUUCAUUAUACAAUUUAAUAUAUAGCGAUCAAGUAAAAUCUGCUUAUUUCGUU ...((((((((((((....)).....((((((((..((.....)).)))))))).))))))))))...................(((((..(((((.....)))))...))))) (-20.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGAAAUAAGCAGAUUUUACUUGAUCGCUAUAUAUUAAAUUGUAUAAUGAAGCUGUUUUUAUUUAAGGUGGUCGUCAUUCUUAAACACAGUGGCCGGUGCAAACAACUCCCCC .........(((.((((......)))))))..........((((((...(..(((((.....(((((((((.....)).))))))).)))))..)..))))))........... (-18.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 50 1 93 31 aact:AA00170|5end_hypothetical_protein_121238..121468_POSITIVE 318 48 1 194 140 aact:AA00201|5end_prolipoprotein_diacylglyceryl_transferase_139740..139970_POSITIVE 305 50 8 209 168 aact:AA01408|5end_conserved_hypothetical_protein_950191..950421_POSITIVE 288 50 3 80 28 aact:AA01243|5end_50S_ribosomal_protein_L17_846974..847204_POSITIVE 283 47 1 191 136 aact:AA02206|5end_tryptophan_synthase,_beta_chain_1501917..1502147_POSITIVE 280 46 1 85 42 aact:AA01303|5end_competence_protein_A_881996..882226_POSITIVE 275 46 1 77 31 aact:AA01370|5end_rod_shape-determining_protein_925436..925666_POSITIVE 272 47 2 184 128 aact:AA01658|5end_maltose_operon_periplasmic_protein_precursor_1124104..1124334_POSITIVE 268 43 3 207 166 aact:AA01029|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_D_719523..719753_POSITIVE 267 49 3 180 134 aact:AA02731|5end_outer_membrane_lipoprotein_carrier_precursor_1911498..1911728_POSITIVE 265 47 1 179 125 aact:AA01107|5end_adenylosuccinate_lyase_762310..762540_POSITIVE 264 49 3 110 59 aact:AA00519|5end_O-acetyltransferase_357139..357369_POSITIVE 263 46 2 195 152 aact:AA01868|5end_biotin_synthetase_1255545..1255775_POSITIVE 261 49 4 79 21 aact:AA01969|5end_hypothetical_protein_1331969..1332199_POSITIVE 261 38 1 57 17 aact:AA01331|5end_50S_ribosomal_protein_L31_898408..898638_POSITIVE 253 48 15 45 8 aact:AA00581|5end_thiosulfate_sulfurtransferase_(rhodanese)_397605..397835_POSITIVE 251 44 1 228 187 aact:AA02613|5end_conserved_hypothetical_protein_1821514..1821744_POSITIVE 251 44 1 103 62 aact:AA02611|5end_hypothetical_protein_1821389..1821619_POSITIVE 251 41 2 189 143 aact:AA02358|5end_homoserine_kinase_1617128..1617358_POSITIVE 249 48 1 218 171 aact:AA01769|5end_hypothetical_protein_1192948..1193178_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 48 1 143 89 aact:AA00200|3end_thymidylate_synthase_139769..139919_POSITIVE 284 47 1 80 45 aact:AA01875|3end_PTS_system,_glucose-specific_enzyme_II,_A_component_1263506..1263656_POSITIVE 280 46 1 104 61 aact:AA01301|3end_competence_protein_B_882095..882245_POSITIVE 275 46 1 74 28 aact:AA01369|3end_rod_shape-determining_protein_925513..925663_POSITIVE 272 47 2 95 39 aact:AA01657|3end_maltose_high-affinity_receptor_1124095..1124245_POSITIVE 264 49 3 104 53 aact:AA00518|3end_conserved_hypothetical_protein_357213..357363_POSITIVE 263 46 2 147 104 aact:AA01867|3end_thiamine_transport_ATP-binding_protein_1255577..1255727_POSITIVE 254 21 1 150 132 aact:AA02601|3end_ATP-dependent_helicase_1813309..1813459_POSITIVE 250 24 1 105 81 aact:AA01614|3end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_1090719..1090869_POSITIVE 250 43 1 148 98 aact:AA01106|3end_conserved_hypothetical_protein_762363..762513_POSITIVE 249 48 1 151 104 aact:AA01767|3end_conserved_hypothetical_protein_1192961..1193111_POSITIVE 249 30 2 116 83 aact:AA00927|3end_ATP-dependent_DNA_helicase_637777..637927_POSITIVE 248 50 4 58 11 aact:AA00448|3end_C-terminal_region_of_competence_protein_M_313058..313208_POSITIVE 246 45 1 139 94 aact:AA01467|3end_mannose-specific_phosphotransferase_system_IID_987214..987364_POSITIVE 242 47 2 150 108 aact:AA02562|3end_adenine_specific_methylase_1785146..1785296_POSITIVE 242 48 13 131 92 aact:AA01651|3end_hypothetical_protein_1120004..1120154_POSITIVE 239 49 1 82 12 aact:AA02420|3end_ISRSO11_related_transposase_1662668..1662818_POSITIVE 237 49 1 131 78 aact:AA02014|3end_probable_hemolysin_1370977..1371127_POSITIVE 236 45 1 69 2 aact:AA00374|3end_short-chain_fatty_acids_transporter_253101..253251_POSITIVE 235 47 1 99 38 aact:AA02217|3end_deoxyribose-phosphate_aldolase_1509835..1509985_POSITIVE