Origin IGS: nnnnntgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt .........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 actaactcctttctaactatcacatttagttctcctaggaactaaataagtttccatgagaactattttaccactttaaaaagagatgtcaagaaaaagtttccatgagaactatcttagtttaaattgacattaggcaagattttttatataataagcgctcactactgtgggtagaaatccattcacttaatgaggagagaaaactttcaaatgaaaccagaagaacaaagatttcttccagcannnnn Mask Tandem Repeat Region ================================================ nnnnntgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt Find is-nt database================================================ Query_seq: SMT_1875:SMT_1876|SMT_1875:SMT_1876:hypothetical protein:transcriptional regulator, MarR family:->->:1833483..1833733 251 nnnnntgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1875:SMT_1876|SMT_1875:SMT_1876:hypothetical protein:transcriptional regulator, MarR family:->->:1833483..1833733 251 nnnnntgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1875:SMT_1876|SMT_1875:SMT_1876:hypothetical protein:transcriptional regulator, MarR family:->->:1833483..1833733 251 nnnnntgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 nnnnntgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 8 End: 127 ....... M E E I F V L L V S F E S F L S S L S E W I S T H S S E R L L Y K K S C L M S I ............................................................................................................................ Protein_Len: 42 Strand: - Start: 1 End: 126 X X S S S I K T R R T E N S L K R E E N L S H I E V W L L S R K N Y L F D Q R I D M ............................................................................................................................. nnnnntgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 92 Start: 97 End: 126 ................................................................................................ATTGACATTAGGCAAGATTTTTTATATAAT............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnntgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -8.3 Tail_Score: -4.17089 Start: 187 End: 225 Full_Region: tctaactatcacatt tagttctcctaggaact aaata agtttccatgagaacta ttttaccactttaaa ..........................................................................................................................................................................................tagttctcctaggaactaaataagtttccatgagaacta.......................... Find igs database================================================ Query_seq: SMT_1875:SMT_1876|SMT_1875:SMT_1876:hypothetical protein:transcriptional regulator, MarR family:->->:1833483..1833733 251 nnnnntgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt Intra-Species Hit: Count: 1 Min: 6 Max: 251 Len: 246 Subject: smit_SMT_1875_SMT_1876|hypothetical protein:transcriptional regulator, MarR family|POSITIVE:POSITIVE|[1833483,1833733]|251 HSP 1 e-value: 1.0E-137 bit: 488.0 Len: 246 Query Start:6 Query End:251 Subject Strand: POSITIVE Subject Start: 6 Subject End: 251 .....tgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt .....tgctggaagaaatctttgttcttctggtttcatttgaaagttttctctcctcattaagtgaatggatttctacccacagtagtgagcgcttattatataaaaaatcttgcctaatgtcaatttaaactaagatagttctcatggaaactttttcttgacatctctttttaaagtggtaaaatagttctcatggaaacttatttagttcctaggagaactaaatgtgatagttagaaaggagttagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUGGAAGAAAUCUUUGUUCUUCUGGUUUCAUUUGAAAGUUUUCUCUCCUCAUUAAGUGAAUGGAUUUCUACCCACAGUAGUGAGCGCUUAUUAUAUAAAAAAUCUUGCCUAAUGUCAAUUUAAACUAAGAUAGUUCUCAUGGAAACUUUUUCUUGACAUCUCUUUUUAAAGUGGUAAAAUAGUUCUCAUGGAAACUUAUUUAGUUCCUAGGAGAACUAAAUGUGAUAGUUAGAAAGGAGUUAGU .((..((((((.......))))))..)).(((...((((((((((....(((((((.(((..(((....)))..)))..))))))).................((((((...(((....))).....)))))).........))))))))))...)))...((((((((.((.((......((((((((..((((.((.....))))))...)))))))).......)).)).))))))))..... (-56.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAACUCCUUUCUAACUAUCACAUUUAGUUCUCCUAGGAACUAAAUAAGUUUCCAUGAGAACUAUUUUACCACUUUAAAAAGAGAUGUCAAGAAAAAGUUUCCAUGAGAACUAUCUUAGUUUAAAUUGACAUUAGGCAAGAUUUUUUAUAUAAUAAGCGCUCACUACUGUGGGUAGAAAUCCAUUCACUUAAUGAGGAGAGAAAACUUUCAAAUGAAACCAGAAGAACAAAGAUUUCUUCCAGCA .....((((.....(((((....((((((((((....)))))))))).((((..((((..((((.((((..((((((....)))).))..))))...))))..))))..))))....)))))........(((((((...(((((((............((((((....)))))))))))))......))))))).)))).......((((....))))...((((((.......))))))..... (-50.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 97 52 71 13 smit:SMT_1608|5end_hypothetical_protein_1597595..1597825_POSITIVE 317 56 12 125 90 smit:SMT_461|5end_mannose-6-phosphate_isomerase_399379..399609_POSITIVE 276 225 183 202 142 smit:SMT_726|5end_ImpB/MucB/SamB_family_protein_631827..632057_NEGATIVE 275 60 20 118 78 smit:SMT_1537|5end_hypothetical_protein_1522668..1522898_NEGATIVE 261 204 163 105 60 smit:SMT_1838|5end_response_regulator_1805400..1805630_NEGATIVE 260 47 2 81 28 smit:SMT_1490|5end_putative_undecaprenyl-phosphate_galactose_phosphotransferase_1470853..1471083_POSITIVE 258 90 46 143 95 smit:SMT_190|5end_preprotein_translocase,_SecY_subunit_124285..124515_POSITIVE 251 89 41 53 1 smit:SMT_747|5end_transcriptional_regulator,_LytR_family_652653..652883_NEGATIVE 243 50 3 120 68 smit:SMT_1972|5end_uncharacterized_conserved_phage_related_protein_1903662..1903892_POSITIVE 242 79 31 129 73 smit:SMT_1788|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1765029..1765259_NEGATIVE 242 79 31 129 73 smit:SMT_1197|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1158751..1158981_NEGATIVE 241 47 1 52 2 smit:SMT_1283|5end_K02240_competence_protein_ComFA_1245667..1245897_POSITIVE 238 55 17 226 181 smit:SMT_141|5end_K03495_glucose_inhibited_division_protein_A_91408..91638_POSITIVE 237 216 181 110 72 smit:SMT_554|5end_K09013_Fe-S_cluster_assembly_ATP-binding_protein_471425..471655_POSITIVE 235 50 4 104 44 smit:SMT_1170|5end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1118126..1118356_NEGATIVE 235 180 131 140 81 smit:SMT_825|5end_aspartate_aminotransferase_749594..749824_NEGATIVE 234 48 1 223 191 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 230 70 21 89 34 smit:SMT_1410|5end_exonuclease_RexA_1392182..1392412_NEGATIVE 230 112 73 101 71 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 226 89 47 120 85 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 97 52 95 37 smit:SMT_1607|3end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1597699..1597849_POSITIVE 281 50 8 63 24 smit:SMT_1936|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1874189..1874339_POSITIVE 275 60 20 117 77 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 261 204 163 93 48 smit:SMT_1839|3end_6-phosphogluconate_dehydrogenase,_decarboxylating_1805412..1805562_NEGATIVE 260 89 69 150 127 smit:SMT_1223|3end_pneumococcal_surface_protein_A_1187151..1187301_NEGATIVE 258 90 46 130 82 smit:SMT_189|3end_50S_ribosomal_protein_L15_124352..124502_POSITIVE 251 89 41 56 4 smit:SMT_748|3end_prephenate_dehydratase_652650..652800_NEGATIVE 248 90 43 80 38 smit:SMT_330|3end_membrane-associated_phospholipid_phosphatase_266187..266337_POSITIVE 235 180 131 143 84 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 235 59 14 139 84 smit:SMT_688|3end_carbamoyl-phosphate_synthase_small_chain_599576..599726_NEGATIVE 230 70 21 92 37 smit:SMT_1411|3end_ATP-dependent_nuclease_subunit_B_1392179..1392329_NEGATIVE 230 112 73 104 74 smit:SMT_1283|3end_K02240_competence_protein_ComFA_1247045..1247195_POSITIVE 226 89 47 77 42 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 226 30 3 129 101 smit:SMT_125|3end_hypothetical_protein_76717..76867_NEGATIVE 225 89 43 150 95 smit:SMT_1005|3end_possible_aluminum_resistance_protein_946679..946829_POSITIVE 224 49 1 102 45 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 223 85 43 128 97 smit:SMT_771|3end_spermidine/putrescine_transport_system_permease_protein_PotB_681356..681506_NEGATIVE 222 47 1 108 54 smit:SMT_1749|3end_anthranilate_synthase_component_II_1728080..1728230_POSITIVE 220 90 46 65 10 smit:SMT_489|3end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_424507..424657_POSITIVE 220 90 56 123 77 smit:SMT_377|3end_hypothetical_protein_315848..315998_POSITIVE