Origin IGS: taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtattatcactcgttttcctttgatttttttattataccactttctcttggagaaactaagtgaaaaacagttggctcactcttttacagcacgatttctagtaaaagttaaagcaccaaatttta Mask Tandem Repeat Region ================================================ taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac Find is-nt database================================================ Query_seq: SMT_1301:SMT_1302|SMT_1301:SMT_1302:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1263897..1264022 126 taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1301:SMT_1302|SMT_1301:SMT_1302:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1263897..1264022 126 taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1301:SMT_1302|SMT_1301:SMT_1302:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1263897..1264022 126 taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 2 End: 124 . F N P A K V K V L F R A T F S H A L Q K E S L K E L L F H Y L L F I L P F R T I M .. taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac 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================================================ taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1301:SMT_1302|SMT_1301:SMT_1302:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1263897..1264022 126 taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: smit_SMT_1301_SMT_1302|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|POSITIVE:POSITIVE|[1263897,1264022]|126 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataatnnnnnnntcaaaggaaaacgagtgataatac taaaatttggtgctttaacttttactagaaatcgtgctgtaaaagagtgagccaactgtttttcacttagtttctccaagagaaagtggtataataaaaaaatcaaaggaaaacgagtgataatac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUUUGGUGCUUUAACUUUUACUAGAAAUCGUGCUGUAAAAGAGUGAGCCAACUGUUUUUCACUUAGUUUCUCCAAGAGAAAGUGGUAUAAUAAAAAAAUCAAAGGAAAACGAGUGAUAAUAC .........(.((((...(((((((.((........)))))))))...))))).((((((((((......((((((...)))))).((((...........))))..))))))).)))........ (-20.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUUAUCACUCGUUUUCCUUUGAUUUUUUUAUUAUACCACUUUCUCUUGGAGAAACUAAGUGAAAAACAGUUGGCUCACUCUUUUACAGCACGAUUUCUAGUAAAAGUUAAAGCACCAAAUUUUA ......(((((..((((((...((...................))....))))))....)))))..........(((....(((((((((........)).)))))))....)))........... (-18.11) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 90 44 116 66 smit:SMT_1907|5end_phosphate-binding_protein_1854105..1854335_POSITIVE 274 73 31 162 119 smit:SMT_91|5end_hypothetical_protein_22578..22808_POSITIVE 268 78 36 222 181 smit:SMT_396|5end_putative_nicotinate_phosphoribosyltransferase_325062..325292_POSITIVE 251 70 28 97 48 smit:SMT_2019|5end_dTDP-glucose_4,6-dehydratase_1937054..1937284_POSITIVE 247 68 24 64 14 smit:SMT_2083|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1982411..1982641_POSITIVE 245 97 65 179 147 smit:SMT_810|5end_oxidoreductase_720015..720245_POSITIVE 243 83 46 230 184 smit:SMT_1234|5end_cadmium_efflux_system_accessory_protein_1194932..1195162_POSITIVE 241 58 11 45 2 smit:SMT_151|5end_K02073_D-methionine_transport_system_substrate-binding_protein_99474..99704_POSITIVE 240 89 44 74 33 smit:SMT_1835|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1803894..1804124_POSITIVE 235 78 31 230 186 smit:SMT_945|5end_cytidylate_kinase_895908..896138_NEGATIVE 235 77 35 83 45 smit:SMT_911|5end_hypothetical_protein_862023..862253_POSITIVE 235 79 31 114 49 smit:SMT_241|5end_hypothetical_protein_predicted_by_Glimmer/Critica_178507..178737_POSITIVE 232 80 46 182 145 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 231 60 11 196 151 smit:SMT_2082|5end_ATP-dependent_nuclease_subunit_B_1982286..1982516_NEGATIVE 231 80 33 105 50 smit:SMT_583|5end_ATP_synthase_F1,_delta_subunit_499497..499727_POSITIVE 230 65 23 68 27 smit:SMT_1611|5end_K05896_segregation_and_condensation_protein_A_1599305..1599535_POSITIVE 230 65 23 68 27 smit:SMT_1034|5end_K05896_segregation_and_condensation_protein_A_977307..977537_NEGATIVE 229 85 46 111 64 smit:SMT_1790|5end_hypothetical_protein_1765644..1765874_POSITIVE 228 58 11 132 96 smit:SMT_1931|5end_23S_rRNA_methyltransferase_1870978..1871208_NEGATIVE 227 79 34 164 122 smit:SMT_939|5end_phosphomethylpyrimidine_kinase_892025..892255_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 73 31 97 54 smit:SMT_90|3end_DNA_polymerase_III_beta_subunit_22593..22743_POSITIVE 268 78 36 107 66 smit:SMT_395|3end_hypothetical_protein_325027..325177_POSITIVE 242 77 31 91 24 smit:SMT_769|3end_spermidine/putrescine-binding_periplasmic_protein_679519..679669_NEGATIVE 236 75 33 86 49 smit:SMT_640|3end_PTS_system,_lactose-specific_IIBC_component_545099..545249_NEGATIVE 233 90 42 82 35 smit:SMT_1570|3end_hypothetical_protein_1563250..1563400_NEGATIVE 231 80 33 105 50 smit:SMT_582|3end_ATP_synthase_F0,_B_subunit_499577..499727_POSITIVE 230 65 23 68 27 smit:SMT_1610|3end_tyrosine_recombinase_1599385..1599535_POSITIVE 226 77 31 91 34 smit:SMT_1414|3end_hypothetical_protein_1397361..1397511_NEGATIVE 224 76 41 86 57 smit:SMT_1337|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1312054..1312204_NEGATIVE 220 87 47 148 109 smit:SMT_823|3end_putative_mucus_binding_protein_740995..741145_NEGATIVE 220 87 47 148 109 smit:SMT_822|3end_putative_mucus_binding_protein_734047..734197_NEGATIVE 220 68 32 110 64 smit:SMT_593|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_510317..510467_POSITIVE 220 78 33 78 36 smit:SMT_174|3end_30S_ribosomal_protein_S19_117792..117942_POSITIVE 217 89 45 74 19 smit:SMT_1395|3end_K07025_putative_hydrolase_of_the_HAD_superfamily_1372082..1372232_POSITIVE 213 96 51 73 20 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 212 53 18 46 9 smit:SMT_2091|3end_hypothetical_protein_1987037..1987187_POSITIVE 211 60 11 137 88 smit:SMT_334|3end_K03713_MerR_family_transcriptional_regulator,_glutamine_synthetase_repressor_273796..273946_POSITIVE 209 66 25 150 112 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 206 80 33 151 96 smit:SMT_1167|3end_aminopeptidase_N_1112593..1112743_NEGATIVE 206 88 42 58 19 smit:SMT_1018|3end_hypothetical_protein_predicted_by_Glimmer/Critica_954739..954889_POSITIVE