Origin IGS: gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggatttttcaagaaaaacgatggtttcaaaagaaactgtcgttttttatagaatgatggcgaagttggaagaaaagtgcttacattttttaaattgtttatcaaatttatgatataatgaatataataaaagttgtgagaagctatttttttaaatcctcttccagtgttaactgaagtatacacatgctaggatgattttataggaggggatgccgtctactgtaaaagtaagataaaactcaataattgataagttcttctttaaatgaagaattcttaactggctatttactaatagggaggtatcatc Mask Tandem Repeat Region ================================================ gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc Find is-nt database================================================ Query_seq: SMT_819:SMT_820|SMT_819:SMT_820:hypothetical protein predicted by Glimmer/Critica:ABC-type oligopeptide transport system, periplasmic component:<-<-:730512..730823 312 gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_819:SMT_820|SMT_819:SMT_820:hypothetical protein predicted by Glimmer/Critica:ABC-type oligopeptide transport system, periplasmic component:<-<-:730512..730823 312 gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_819:SMT_820|SMT_819:SMT_820:hypothetical protein predicted by Glimmer/Critica:ABC-type oligopeptide transport system, periplasmic component:<-<-:730512..730823 312 gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 37 End: 141 .................................... M L H L K K N L S I I E F Y L T F T V D G I P S Y K I I L A C V Y F S ........................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 128 End: 310 ............................................................................................................................... M Y T S V N T G R G F K K I A S H N F Y Y I H Y I I N L I N N L K N V S T F L P T S P S F Y K K R Q F L L K P S F F L K .. Protein_Len: 30 Strand: - Start: 204 End: 293 ........................................................................................................................................................................................................... L N S L C N L F H L C K E E L K A M M R Y F V V T E K S V M ................... gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc 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================================================ gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -3.8 Tail_Score: -5.06816 Start: 272 End: 295 Full_Region: TCATTCTATAAAAAA CGACAGTTTC TTTT GAAACCATCG TTTTTCTTGAAAAAT ...............................................................................................................................................................................................................................................................................CGACAGTTTCTTTTGAAACCATCG................. Find igs database================================================ Query_seq: SMT_819:SMT_820|SMT_819:SMT_820:hypothetical protein predicted by Glimmer/Critica:ABC-type oligopeptide transport system, periplasmic component:<-<-:730512..730823 312 gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc Intra-Species Hit: Count: 1 Min: 1 Max: 312 Len: 312 Subject: smit_SMT_819_SMT_820|hypothetical protein predicted by Glimmer/Critica:ABC-type oligopeptide transport system, periplasmic component|NEGATIVE:NEGATIVE|[730512,730823]|312 HSP 1 e-value: 1.0E-164 bit: 577.0 Len: 312 Query Start:1 Query End:312 Subject Strand: POSITIVE Subject Start: 1 Subject End: 312 gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttnnnnnnntagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc gatgatacctccctattagtaaatagccagttaagaattcttcatttaaagaagaacttatcaattattgagttttatcttacttttacagtagacggcatcccctcctataaaatcatcctagcatgtgtatacttcagttaacactggaagaggatttaaaaaaatagcttctcacaacttttattatattcattatatcataaatttgataaacaatttaaaaaatgtaagcacttttcttccaacttcgccatcattctataaaaaacgacagtttcttttgaaaccatcgtttttcttgaaaaatcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAUACCUCCCUAUUAGUAAAUAGCCAGUUAAGAAUUCUUCAUUUAAAGAAGAACUUAUCAAUUAUUGAGUUUUAUCUUACUUUUACAGUAGACGGCAUCCCCUCCUAUAAAAUCAUCCUAGCAUGUGUAUACUUCAGUUAACACUGGAAGAGGAUUUAAAAAAAUAGCUUCUCACAACUUUUAUUAUAUUCAUUAUAUCAUAAAUUUGAUAAACAAUUUAAAAAAUGUAAGCACUUUUCUUCCAACUUCGCCAUCAUUCUAUAAAAAACGACAGUUUCUUUUGAAACCAUCGUUUUUCUUGAAAAAUCC ((((((......(((((.(((((.....(((.(((....))).)))..((((((((((((........)))))))).))))...))))))))))..((.....)).........))))))...((..((((..((....))..)))).(((((((.((((....)))).((((...(((..(((((....(((.....(((((......)))))...))).)))))..)))))))....)))))))......)).....(((....((((((((..(((((....)))))..))))))))...)))...... (-50.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUUUUUCAAGAAAAACGAUGGUUUCAAAAGAAACUGUCGUUUUUUAUAGAAUGAUGGCGAAGUUGGAAGAAAAGUGCUUACAUUUUUUAAAUUGUUUAUCAAAUUUAUGAUAUAAUGAAUAUAAUAAAAGUUGUGAGAAGCUAUUUUUUUAAAUCCUCUUCCAGUGUUAACUGAAGUAUACACAUGCUAGGAUGAUUUUAUAGGAGGGGAUGCCGUCUACUGUAAAAGUAAGAUAAAACUCAAUAAUUGAUAAGUUCUUCUUUAAAUGAAGAAUUCUUAACUGGCUAUUUACUAAUAGGGAGGUAUCAUC ..((((((((.((((((((((((((((....)))))))))))))))).......((((((....(((((((((.(((.((((((.((((((...(((((((((......)))).....)))))...)))))).))))))..))).))))))))).((((((((((((....)))).(((((....)))))..............)))))))).))))))...)).))))))..((((...(((...........((((((((.......)))))))).........(((((....))))).))).))))... (-77.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 929 140 91 231 182 smit:SMT_819|5end_hypothetical_protein_predicted_by_Glimmer/Critica_730421..730651_NEGATIVE 318 129 82 131 76 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 271 158 115 227 187 smit:SMT_1957|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1890645..1890875_POSITIVE 262 114 71 114 74 smit:SMT_1136|5end_K02025_multiple_sugar_transport_system_permease_protein_1078101..1078331_NEGATIVE 258 282 243 77 28 smit:SMT_1470|5end_K06188_aquaporin_Z_1452560..1452790_POSITIVE 254 279 233 119 74 smit:SMT_2074|5end_dTDP-glucose_4,6-dehydratase_1977021..1977251_POSITIVE 249 105 70 56 28 smit:SMT_232|5end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_168246..168476_POSITIVE 248 132 97 230 190 smit:SMT_990|5end_hypothetical_protein_933947..934177_NEGATIVE 247 117 71 207 167 smit:SMT_230|5end_hypothetical_protein_predicted_by_Glimmer/Critica_165830..166060_NEGATIVE 245 303 261 98 65 smit:SMT_337|5end_hypothetical_protein_275539..275769_POSITIVE 244 150 101 93 24 smit:SMT_952|5end_hypothetical_protein_900912..901142_NEGATIVE 242 140 94 126 59 smit:SMT_1915|5end_pyridoxine_biosynthesis_protein_1860329..1860559_POSITIVE 242 150 104 112 69 smit:SMT_1263|5end_hypothetical_protein_1228104..1228334_POSITIVE 242 132 93 69 22 smit:SMT_437|5end_transcriptional_regulator,_TetR_family_378402..378632_POSITIVE 242 138 91 102 51 smit:SMT_222|5end_beta-glucosidase_154971..155201_POSITIVE 239 160 114 166 121 smit:SMT_190|5end_preprotein_translocase,_SecY_subunit_124285..124515_POSITIVE 237 110 75 107 69 smit:SMT_493|5end_K01996_branched-chain_amino_acid_transport_system_ATP-binding_protein_427137..427367_POSITIVE 235 126 88 110 63 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 234 128 83 92 37 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 233 263 229 41 8 smit:SMT_2064|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1972182..1972412_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 129 82 144 89 smit:SMT_1455|3end_deoxyribose-phosphate_aldolase_1437873..1438023_NEGATIVE 258 282 243 69 20 smit:SMT_1469|3end_GTP_pyrophosphokinase_1452632..1452782_POSITIVE 254 279 233 92 47 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 248 132 97 144 104 smit:SMT_991|3end_hypothetical_protein_934033..934183_NEGATIVE 245 303 261 101 68 smit:SMT_336|3end_hypothetical_protein_275622..275772_POSITIVE 244 150 101 106 37 smit:SMT_953|3end_hypothetical_protein_900899..901049_NEGATIVE 242 150 104 110 67 smit:SMT_1262|3end_ribosomal_protein_L11_methyltransferase_1228182..1228332_POSITIVE 242 109 72 88 45 smit:SMT_364|3end_ribosome-binding_factor_A_301353..301503_POSITIVE 238 149 103 140 72 smit:SMT_496|3end_superoxide_dismutase,_manganese-dependent_431118..431268_POSITIVE 238 303 275 42 12 smit:SMT_163|3end_cardiolipin_synthetase_108936..109086_POSITIVE 237 110 75 107 69 smit:SMT_492|3end_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_427217..427367_POSITIVE 235 126 88 67 20 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 234 109 80 122 99 smit:SMT_913|3end_putative_sucrose-specific_PTS_permease,_enzyme_II_863923..864073_NEGATIVE 234 128 83 99 44 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 232 147 116 76 43 smit:SMT_1785|3end_phenylalanyl-tRNA_synthetase_beta_chain_1762327..1762477_NEGATIVE 229 274 238 127 102 smit:SMT_1580|3end_MutT/NUDIX_family_protein_1573153..1573303_POSITIVE 229 109 61 115 65 smit:SMT_896|3end_hypothetical_protein_843119..843269_NEGATIVE 229 48 2 93 31 smit:SMT_353|3end_immunity_protein_BlpL_291364..291514_POSITIVE 227 263 226 128 96 smit:SMT_184|3end_30S_ribosomal_protein_S8_121891..122041_POSITIVE 223 305 273 61 30 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE