Origin IGS: tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttagaactcctttgtttaatgatgatttatcttcccagcacnnnnnttaattaattaannnnnacgctttccttgtatttgttcagaaaaaaccaacctcaaggctggtttcttttayata Mask Tandem Repeat Region ================================================ tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac Find is-nt database================================================ Query_seq: SMT_1002:SMT_1003|SMT_1002:SMT_1003:aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B:hypothetical protein:->->:945210..945332 123 tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1002:SMT_1003|SMT_1002:SMT_1003:aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B:hypothetical protein:->->:945210..945332 123 tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1002:SMT_1003|SMT_1002:SMT_1003:aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B:hypothetical protein:->->:945210..945332 123 tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac Predict ORF larger than 30AA ================================================ tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac 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================================================ tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1002:SMT_1003|SMT_1002:SMT_1003:aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B:hypothetical protein:->->:945210..945332 123 tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: smit_SMT_1002_SMT_1003|aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B:hypothetical protein|POSITIVE:POSITIVE|[945210,945332]|123 HSP 1 e-value: 3.0E-45 bit: 181.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac tatrtaaaagaaaccagccttgaggttggttttttctgaacaaatacaaggaaagcgtnnnnnttaattaattaannnnngtgctgggaagataaatcatcattaaacaaaggagttctaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAURUAAAAGAAACCAGCCUUGAGGUUGGUUUUUUCUGAACAAAUACAAGGAAAGCGUNNNNNUUAAUUAAUUAANNNNNGUGCUGGGAAGAUAAAUCAUCAUUAAACAAAGGAGUUCUAAAC .......((((((((((((....))))))))))))..((((............((((......((((....))))......)))).....(((.....))).............))))..... (-20.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUAGAACUCCUUUGUUUAAUGAUGAUUUAUCUUCCCAGCACNNNNNUUAAUUAAUUAANNNNNACGCUUUCCUUGUAUUUGUUCAGAAAAAACCAACCUCAAGGCUGGUUUCUUUUAYAUA .....((((.....((((....((((...)))).....)))).........................((.......))....)))).((((((((((.((....)).)))))).))))..... (-12.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 55 13 57 15 smit:SMT_1619|5end_K02006_cobalt_transport_system_ATP-binding_protein_1606526..1606756_NEGATIVE 263 102 64 139 97 smit:SMT_228|5end_hypothetical_protein_164384..164614_POSITIVE 247 120 81 173 134 smit:SMT_1068|5end_ATP-dependent_DNA_helicase_RecG_1006891..1007121_POSITIVE 241 38 11 66 27 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 240 47 13 87 47 smit:SMT_1329|5end_GTP-binding_protein_CgtA_1305788..1306018_NEGATIVE 240 58 12 219 166 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 231 120 82 167 131 smit:SMT_491|5end_K01998_branched-chain_amino_acid_transport_system_permease_protein_425417..425647_POSITIVE 228 58 14 163 118 smit:SMT_1718|5end_Holliday_junction_DNA_helicase_RuvA_1704877..1705107_NEGATIVE 224 57 12 97 52 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 223 56 14 98 60 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 223 56 14 198 160 smit:SMT_1666|5end_hypothetical_protein_1657467..1657697_NEGATIVE 218 57 17 46 12 smit:SMT_2142|5end_hypothetical_protein_predicted_by_Glimmer/Critica_2019999..2020229_POSITIVE 216 58 11 83 42 smit:SMT_1866|5end_extramembranal_protein_1827290..1827520_POSITIVE 216 58 11 83 42 smit:SMT_1313|5end_extramembranal_protein_1277274..1277504_POSITIVE 214 104 64 165 127 smit:SMT_2039|5end_malolactic_enzyme_1950427..1950657_NEGATIVE 213 58 15 43 1 smit:SMT_1405|5end_tyrosine_recombinase_1383150..1383380_NEGATIVE 211 58 19 189 151 smit:SMT_1988|5end_two-component_sensor_kinase_YesM_1916804..1917034_NEGATIVE 211 45 13 163 135 smit:SMT_365|5end_hypothetical_protein_301485..301715_POSITIVE 210 58 14 62 24 smit:SMT_1184|5end_phosphotransferase_system,_mannose/fructose/N-acetylgalactosamine-specific_component_IIB_1142037..1142267_NEGATIVE 209 90 48 216 177 smit:SMT_1008|5end_hypothetical_protein_948021..948251_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 35 8 83 56 smit:SMT_1002|3end_aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B_945149..945299_POSITIVE 266 34 5 92 65 smit:SMT_1146|3end_maltose_operon_transcriptional_repressor_1091202..1091352_POSITIVE 263 102 64 93 51 smit:SMT_227|3end_hypothetical_protein_164418..164568_POSITIVE 244 92 64 115 87 smit:SMT_1816|3end_K02026_multiple_sugar_transport_system_permease_protein_1791504..1791654_POSITIVE 241 38 11 54 15 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 237 35 9 83 59 smit:SMT_1147|3end_hypothetical_protein_1091203..1091353_NEGATIVE 235 101 81 136 115 smit:SMT_1067|3end_alanine_racemase_1006952..1007102_POSITIVE 228 58 14 147 102 smit:SMT_1719|3end_DNA_mismatch_repair_protein_1704893..1705043_NEGATIVE 227 35 6 68 39 smit:SMT_270|3end_ATP-binding_subunit_of_Clp_protease_and_DnaK/DnaJ_chaperones_211225..211375_POSITIVE 223 56 14 42 4 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 220 106 64 42 5 smit:SMT_1070|3end_hypothetical_protein_1009644..1009794_NEGATIVE 216 58 11 90 49 smit:SMT_1865|3end_D-alanyl_carrier_protein_1827377..1827527_POSITIVE 216 58 11 90 49 smit:SMT_1312|3end_D-alanyl_carrier_protein_1277361..1277511_POSITIVE 214 104 64 129 91 smit:SMT_2040|3end_transcription-repair_coupling_factor_1950463..1950613_NEGATIVE 210 58 14 65 27 smit:SMT_1185|3end_beta-galactosidase_1142034..1142184_NEGATIVE 208 56 13 57 20 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE 206 50 11 136 101 smit:SMT_966|3end_transcriptional_regulator,_TetR_family_911568..911718_NEGATIVE 205 56 16 90 38 smit:SMT_742|3end_hypothetical_protein_645784..645934_NEGATIVE 202 46 15 73 33 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 201 89 49 112 72 smit:SMT_2043|3end_putative_mucus_binding_protein_1954013..1954163_NEGATIVE