Origin IGS: gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc .........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 gagaaactcctttcggcatgtatctttgttttcgctttcattatatattttttattgctagatgataagggacagattctattatttgtccccttttaaacccgtttaaaacatttttttggtaaaatgaagtaagtaaaagaaaggcttcctatggcatcatcacttattacaaaaaaacggattacaaggcatttagagaccttttagctactagagaatttgacaaaatctccattgtagatatc Mask Tandem Repeat Region ================================================ gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc Find is-nt database================================================ Query_seq: SMT_1390:SMT_1391|SMT_1390:SMT_1391:hypothetical protein:dihydroxyacetone kinase:<-->:1367412..1367659 248 gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1390:SMT_1391|SMT_1390:SMT_1391:hypothetical protein:dihydroxyacetone kinase:<-->:1367412..1367659 248 gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1390:SMT_1391|SMT_1390:SMT_1391:hypothetical protein:dihydroxyacetone kinase:<-->:1367412..1367659 248 gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 1 End: 90 I D V I S I K D F E R T A L L D R F A K Y D T K K Y Y T I M .............................................................................................................................................................. gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc 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: 81 Start: 180 End: 209 ...................................................................................................................................................................................CTTATCATCTAGCAATAAAAAATATATAAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 59 HP_score: -4.0 Tail_Score: -4.10453 Start: 156 End: 181 Full_Region: tattgctagatgata agggacagat tctatt atttgtcccc ttttaaacccgttta ...........................................................................................................................................................agggacagattctattatttgtcccc................................................................... TransTerm Strand: + Conf: 57 HP_score: -5.3 Tail_Score: -3.4678 Start: 157 End: 180 Full_Region: AAACGGGTTTAAAAG GGGACAAAT AATAGA ATCTGTCCC TTATCATCTAGCAAT ............................................................................................................................................................GGGACAAATAATAGAATCTGTCCC.................................................................... TransTerm Strand: - Conf: 65 HP_score: -7.5 Tail_Score: -3.0579 Start: 157 End: 180 Full_Region: attgctagatgataa gggacagat tctatt atttgtccc cttttaaacccgttt ............................................................................................................................................................gggacagattctattatttgtccc.................................................................... Find igs database================================================ Query_seq: SMT_1390:SMT_1391|SMT_1390:SMT_1391:hypothetical protein:dihydroxyacetone kinase:<-->:1367412..1367659 248 gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc Intra-Species Hit: Count: 1 Min: 1 Max: 248 Len: 248 Subject: smit_SMT_1390_SMT_1391|hypothetical protein:dihydroxyacetone kinase|NEGATIVE:POSITIVE|[1367412,1367659]|248 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 248 Query Start:1 Query End:248 Subject Strand: POSITIVE Subject Start: 1 Subject End: 248 gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgnnnnnnngtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccnnnnnnntgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc gatatctacaatggagattttgtcaaattctctagtagctaaaaggtctctaaatgccttgtaatccgtttttttgtaataagtgatgatgccataggaagcctttcttttacttacttcattttaccaaaaaaatgttttaaacgggtttaaaaggggacaaataatagaatctgtcccttatcatctagcaataaaaaatatataatgaaagcgaaaacaaagatacatgccgaaaggagtttctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUCUACAAUGGAGAUUUUGUCAAAUUCUCUAGUAGCUAAAAGGUCUCUAAAUGCCUUGUAAUCCGUUUUUUUGUAAUAAGUGAUGAUGCCAUAGGAAGCCUUUCUUUUACUUACUUCAUUUUACCAAAAAAAUGUUUUAAACGGGUUUAAAAGGGGACAAAUAAUAGAAUCUGUCCCUUAUCAUCUAGCAAUAAAAAAUAUAUAAUGAAAGCGAAAACAAAGAUACAUGCCGAAAGGAGUUUCUC ..(((((....((((((...........))))))...((((..............((((..(((..((((((((((....((((((.........(((((....))))).........))))))...))))))))))..)))...)))).....((((((((.((......)).))))))))......))))...............................)))))....((....))........ (-47.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAAACUCCUUUCGGCAUGUAUCUUUGUUUUCGCUUUCAUUAUAUAUUUUUUAUUGCUAGAUGAUAAGGGACAGAUUCUAUUAUUUGUCCCCUUUUAAACCCGUUUAAAACAUUUUUUUGGUAAAAUGAAGUAAGUAAAAGAAAGGCUUCCUAUGGCAUCAUCACUUAUUACAAAAAAACGGAUUACAAGGCAUUUAGAGACCUUUUAGCUACUAGAGAAUUUGACAAAAUCUCCAUUGUAGAUAUC ......(((......((.((((..((((((((..(((((.((((.((((((...((((((((......(((((((((......))))))))).(((((((....)))))))......))))))))...)))))).))))..)))))(((......)))..................)))))))).))))..)).....))).........((((..((((.(((....)))))))....))))..... (-47.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 837 70 21 161 112 smit:SMT_1390|5end_hypothetical_protein_1367321..1367551_NEGATIVE 270 119 76 208 167 smit:SMT_398|5end_hypothetical_protein_327651..327881_POSITIVE 266 69 31 192 152 smit:SMT_1689|5end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1671542..1671772_POSITIVE 263 192 154 55 11 smit:SMT_181|5end_50S_ribosomal_protein_L24_120125..120355_POSITIVE 257 70 25 67 26 smit:SMT_718|5end_NADP-specific_glutamate_dehydrogenase_623176..623406_POSITIVE 253 129 81 90 39 smit:SMT_1318|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1283511..1283741_POSITIVE 248 57 11 89 47 smit:SMT_789|5end_hypothetical_protein_701072..701302_NEGATIVE 242 78 32 47 9 smit:SMT_141|5end_K03495_glucose_inhibited_division_protein_A_91408..91638_POSITIVE 237 59 17 167 114 smit:SMT_975|5end_hypothetical_protein_922953..923183_POSITIVE 237 69 26 91 42 smit:SMT_442|5end_transcriptional_regulator,_putative_381652..381882_POSITIVE 236 129 81 154 105 smit:SMT_1998|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1921868..1922098_POSITIVE 233 79 36 72 40 smit:SMT_1655|5end_glucose-6-phosphate_1-dehydrogenase_1645021..1645251_NEGATIVE 233 197 153 79 23 smit:SMT_1526|5end_K07720_two-component_system,_response_regulator_YesN_1510554..1510784_NEGATIVE 233 140 91 142 87 smit:SMT_1474|5end_K02003_1455170..1455400_POSITIVE 227 130 82 181 145 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 225 120 91 193 166 smit:SMT_1835|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1803894..1804124_POSITIVE 225 131 96 178 136 smit:SMT_354|5end_hypothetical_protein_291343..291573_POSITIVE 223 115 73 110 69 smit:SMT_364|5end_ribosome-binding_factor_A_300923..301153_POSITIVE 222 74 33 206 165 smit:SMT_1538|5end_two-component_response_regulator_YvqC_1523301..1523531_NEGATIVE 220 119 71 116 57 smit:SMT_1912|5end_D-alanyl-D-alanine_carboxypeptidase_1857920..1858150_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 129 81 86 35 smit:SMT_1317|3end_glycosyltransferase_1283587..1283737_POSITIVE 248 57 11 68 26 smit:SMT_790|3end_hypothetical_protein_701093..701243_NEGATIVE 248 126 92 57 27 smit:SMT_397|3end_NAD(+)_synthetase_327423..327573_POSITIVE 242 78 32 57 19 smit:SMT_140|3end_NUDIX_family_hydrolase_91498..91648_POSITIVE 241 105 66 118 82 smit:SMT_1019|3end_K03295_cation_efflux_system_protein,_CDF_family_954782..954932_NEGATIVE 233 197 153 67 11 smit:SMT_1527|3end_two-component_sensor_kinase_1510566..1510716_NEGATIVE 230 92 55 146 112 smit:SMT_694|3end_putative_ATP-binding_component_of_a_transport_system_605968..606118_POSITIVE 229 69 30 46 3 smit:SMT_1979|3end_possible_cell_surface_protein_1910282..1910432_NEGATIVE 225 131 96 119 77 smit:SMT_353|3end_immunity_protein_BlpL_291364..291514_POSITIVE 222 89 41 109 46 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 220 108 61 92 49 smit:SMT_1858|3end_K03497_chromosome_partitioning_protein,_ParB_family_1821687..1821837_NEGATIVE 220 103 67 135 100 smit:SMT_1617|3end_K02015_iron_complex_transport_system_permease_protein_1603544..1603694_NEGATIVE 219 110 64 92 41 smit:SMT_1604|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1595163..1595313_POSITIVE 219 127 82 99 34 smit:SMT_1170|3end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1117569..1117719_NEGATIVE 217 68 22 96 39 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 216 103 62 142 92 smit:SMT_1846|3end_acyl-ACP_thioesterase,_putative_1812227..1812377_POSITIVE 214 110 67 144 107 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE 214 58 14 102 60 smit:SMT_1534|3end_signal_peptidase_I_1517912..1518062_POSITIVE 214 110 67 144 107 smit:SMT_1466|3end_endopeptidase_O_1447905..1448055_POSITIVE 214 77 31 112 75 smit:SMT_539|3end_sensor_histidine_kinase_CiaH_456059..456209_POSITIVE