Origin IGS: agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atagataagcaatcttcacaacgaatataaaattaaaacgtgcaaatcattttcaagaggctttagatttcttgtattttaaaagaaactaaagccttttgtggatgtattgtttttcagaaagtatgaaaaactagagagttgtatcggggagataaatattatttcgcttaaataaattaggagtcgttttattct Mask Tandem Repeat Region ================================================ agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat Find is-nt database================================================ Query_seq: SMT_1206:SMT_1207|SMT_1206:SMT_1207:similar to sensor histidine kinase (AgrC from Staphylococcus):choline binding protein A:<-<-:1167134..1167331 198 agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1206:SMT_1207|SMT_1206:SMT_1207:similar to sensor histidine kinase (AgrC from Staphylococcus):choline binding protein A:<-<-:1167134..1167331 198 agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1206:SMT_1207|SMT_1206:SMT_1207:similar to sensor histidine kinase (AgrC from Staphylococcus):choline binding protein A:<-<-:1167134..1167331 198 agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 4 End: 117 ... M K R L L I Y L S E I I F I S P I Q L S S F S Y F L K N N T S T K G F S F F ................................................................................. agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat 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================================================ agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.9 Tail_Score: -4.46757 Start: 103 End: 140 Full_Region: aaatcattttcaaga ggctttagatttcttgta ttt taaaagaaactaaagcc ttttgtggatgtatt ......................................................................................................ggctttagatttcttgtattttaaaagaaactaaagcc.......................................................... Find igs database================================================ Query_seq: SMT_1206:SMT_1207|SMT_1206:SMT_1207:similar to sensor histidine kinase (AgrC from Staphylococcus):choline binding protein A:<-<-:1167134..1167331 198 agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat Intra-Species Hit: Count: 2 Min: 1 Max: 198 Len: 198 Subject: smit_SMT_1986_SMT_1987|mercuric reductase:hypothetical protein predicted by Glimmer/Critica|POSITIVE:NEGATIVE|[1915622,1916061]|440 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 243 Subject End: 440 agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat Subject: smit_SMT_1206_SMT_1207|similar to sensor histidine kinase (AgrC from Staphylococcus):choline binding protein A|NEGATIVE:NEGATIVE|[1167134,1167331]|198 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat agaataaaacgactcctaatttatttaagcgaaataatatttatctccccgatacaactctctagtttttcatactttctgaaaaacaatacatccacaaaaggctttagtttcttttaaaatacaagaaatctaaagcctcttgaaaatgatttgcacgttttaattttatattcgttgtgaagattgcttatctat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUAAAACGACUCCUAAUUUAUUUAAGCGAAAUAAUAUUUAUCUCCCCGAUACAACUCUCUAGUUUUUCAUACUUUCUGAAAAACAAUACAUCCACAAAAGGCUUUAGUUUCUUUUAAAAUACAAGAAAUCUAAAGCCUCUUGAAAAUGAUUUGCACGUUUUAAUUUUAUAUUCGUUGUGAAGAUUGCUUAUCUAU (((.(((((((.....(((.....))).(((((........((((.....))))..........((((((((.......))))))))....(((...(((.(((((((((((((((.........)))))).))))))))).)))...))).))))).))))))).(((((((.....)))))))........))).. (-36.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGAUAAGCAAUCUUCACAACGAAUAUAAAAUUAAAACGUGCAAAUCAUUUUCAAGAGGCUUUAGAUUUCUUGUAUUUUAAAAGAAACUAAAGCCUUUUGUGGAUGUAUUGUUUUUCAGAAAGUAUGAAAAACUAGAGAGUUGUAUCGGGGAGAUAAAUAUUAUUUCGCUUAAAUAAAUUAGGAGUCGUUUUAUUCU ..(((.((((...((((......................((((((..((((..(((((((((((((.((((((.........)))))))))))))))))))..))))....((((((((.......)))))))).......)))))).((.((((((.....)))))).))...........))))..))))...))) (-48.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 783 90 41 181 132 smit:SMT_1206|5end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1167043..1167273_NEGATIVE 269 116 87 54 20 smit:SMT_1160|5end_K03152_4-methyl-5(b-hydroxyethyl)-thiazole_monophosphate_biosynthesis_1105174..1105404_NEGATIVE 263 88 44 127 85 smit:SMT_711|5end_choline_kinase_620170..620400_NEGATIVE 263 88 44 127 85 smit:SMT_681|5end_choline_kinase_590821..591051_NEGATIVE 237 150 101 209 148 smit:SMT_1359|5end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1338003..1338233_NEGATIVE 232 164 127 128 93 smit:SMT_1012|5end_xanthine_permease_949154..949384_POSITIVE 226 57 24 206 176 smit:SMT_576|5end_transcriptional_regulator,_LysR_family_495157..495387_POSITIVE 224 128 97 228 195 smit:SMT_1731|5end_K06442_putative_hemolysin_1715643..1715873_POSITIVE 217 79 43 225 190 smit:SMT_1866|5end_extramembranal_protein_1827290..1827520_POSITIVE 217 79 43 225 190 smit:SMT_1313|5end_extramembranal_protein_1277274..1277504_POSITIVE 213 54 11 59 16 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 212 173 134 70 29 smit:SMT_337|5end_hypothetical_protein_275539..275769_POSITIVE 210 190 141 191 144 smit:SMT_1718|5end_Holliday_junction_DNA_helicase_RuvA_1704877..1705107_NEGATIVE 209 80 31 218 172 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 208 79 42 38 4 smit:SMT_351|5end_hypothetical_protein_290289..290519_POSITIVE 207 146 101 196 164 smit:SMT_416|5end_ribonuclease_Z_359423..359653_POSITIVE 206 79 42 180 142 smit:SMT_707|5end_hypothetical_protein_predicted_by_Glimmer/Critica_617120..617350_NEGATIVE 205 162 131 62 29 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 205 82 55 164 141 smit:SMT_98|5end_hypothetical_protein_28924..29154_POSITIVE 205 82 55 49 26 smit:SMT_97|5end_hypothetical_protein_28809..29039_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 731 180 131 72 23 smit:SMT_1987|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1915972..1916122_NEGATIVE 269 116 87 43 9 smit:SMT_1161|3end_K05837_rod_shape_determining_protein_RodA_1105185..1105335_NEGATIVE 263 88 44 110 68 smit:SMT_712|3end_alcohol_dehydrogenase,_zinc-containing_620187..620337_NEGATIVE 263 88 44 110 68 smit:SMT_682|3end_hypothetical_protein_590838..590988_NEGATIVE 232 164 127 128 93 smit:SMT_1011|3end_xanthine_phosphoribosyltransferase_949234..949384_POSITIVE 228 147 101 111 55 smit:SMT_1945|3end_putative_dihydrolipoamide_S-acetyltransferase_1880646..1880796_POSITIVE 224 78 37 70 23 smit:SMT_1804|3end_hypothetical_protein_1780314..1780464_POSITIVE 212 173 134 73 32 smit:SMT_336|3end_hypothetical_protein_275622..275772_POSITIVE 209 80 31 108 62 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 205 162 131 69 36 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 205 82 55 44 21 smit:SMT_96|3end_hypothetical_protein_28884..29034_POSITIVE 202 68 30 52 23 smit:SMT_84|3end_predicted_signal_transduction_protein_with_a_C-terminal_ATPase_domain_15292..15442_NEGATIVE 200 76 40 110 70 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 199 57 13 54 12 smit:SMT_1209|3end_choline_binding_protein_PcpA_1169779..1169929_NEGATIVE 198 180 131 90 38 smit:SMT_1338|3end_K05832_putative_ABC_transport_system_permease_protein_1312809..1312959_NEGATIVE 198 177 144 63 22 smit:SMT_1231|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1193034..1193184_POSITIVE 196 81 45 112 69 smit:SMT_340|3end_chaperone_protein_280566..280716_POSITIVE 191 97 55 64 16 smit:SMT_1169|3end_phosphorylase,_Pnp/UDP_family_1116586..1116736_NEGATIVE 191 122 88 101 64 smit:SMT_419|3end_hypothetical_protein_predicted_by_Glimmer/Critica_362510..362660_POSITIVE 191 60 13 125 77 smit:SMT_410|3end_glucokinase_355477..355627_POSITIVE