Origin IGS: aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac .........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 gtttattttctcctgttaaattgtcaggccagaacggccagttttcacggggttcagatacttatttagttcaagagctgaactgaacacgctctaagaactgtgcaaaatagataagttggcttgtttgtaaacaaacttctccaactttctaattttgctttgttctttacgagctttgtatcttgatt Mask Tandem Repeat Region ================================================ aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Find is-nt database================================================ Query_seq: SMT_184:SMT_185|SMT_184:SMT_185:30S ribosomal protein S8:50S ribosomal protein L6:->->:121952..122142 191 aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_184:SMT_185|SMT_184:SMT_185:30S ribosomal protein S8:50S ribosomal protein L6:->->:121952..122142 191 aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_184:SMT_185|SMT_184:SMT_185:30S ribosomal protein S8:50S ribosomal protein L6:->->:121952..122142 191 aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Predict ORF larger than 30AA ================================================ aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac 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================================================ aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_184:SMT_185|SMT_184:SMT_185:30S ribosomal protein S8:50S ribosomal protein L6:->->:121952..122142 191 aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: smit_SMT_184_SMT_185|30S ribosomal protein S8:50S ribosomal protein L6|POSITIVE:POSITIVE|[121952,122142]|191 HSP 1 e-value: 1.0E-104 bit: 379.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Inter-species Hit: Count: 4 Min: 1 Max: 191 Len: 191 Subject: NC_003028_SP_0224_SP_0225|30S ribosomal protein S8:50S ribosomal protein L6|POSITIVE:POSITIVE|[200627,200817]|191 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac aatcaagatacaaagctcgtaaagaacaaagcaaaattaggaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Subject: NC_008533_SPD_0207_SPD_0208|ribosomal protein S8:ribosomal protein L6|POSITIVE:POSITIVE|[203136,203326]|191 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac aatcaagatacaaagctcgtaaagaacaaagcaaaattaggaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagatcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Subject: NC_003098_spr0203_spr0204|30S ribosomal protein S8:50S ribosomal protein L6|POSITIVE:POSITIVE|[203136,203326]|191 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 aatcaagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac aatcaagatacaaagctcgtaaagaacaaagcaaaattaggaagttggagaagtttgtttacaaacaagccaacttatctattttgcacagttcttagatcgtgttcagttcagctcttgaactaaataagtatctgaaccccgtgaaaactggccgttctggcctgacaatttaacaggagaaaataaac Subject: NC_004350_SMU.2011_SMU.2012|50S ribosomal protein L6:30S ribosomal protein S8|NEGATIVE:NEGATIVE|[1887284,1887695]|412 HSP 1 e-value: 9.0E-30 bit: 131.0 Len: 125 Query Start:5 Query End:129 Subject Strand: NEGATIVE Subject Start: 284 Subject End: 408 ....aagatacaaagctcgtaaagaacaaagcaaaattagaaagttggagaagtttgtttacaaacaa-gccaacttatctattttgcacagttcttagagcgtgttcagttcagctcttgaactaaata.............................................................. ....aagatacaaagcttgtaaagaacaaagcaaa-ttaggaagttggagcagtttgtttacaaaaaaagtccacttatctattttgcacagttctcagagcgtgttcagtttaactattaaactaaata.............................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCAAGAUACAAAGCUCGUAAAGAACAAAGCAAAAUUAGAAAGUUGGAGAAGUUUGUUUACAAACAAGCCAACUUAUCUAUUUUGCACAGUUCUUAGAGCGUGUUCAGUUCAGCUCUUGAACUAAAUAAGUAUCUGAACCCCGUGAAAACUGGCCGUUCUGGCCUGACAAUUUAACAGGAGAAAAUAAAC ..(((.(((((...((((...((((((...(((((((.((((((((((....(((((....)))))...))))))).))))))))))...)))))).)))).((((.(((((((...))))))).)))).))))))))...((.((((....((((.....))))......))))...))........... (-56.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUAUUUUCUCCUGUUAAAUUGUCAGGCCAGAACGGCCAGUUUUCACGGGGUUCAGAUACUUAUUUAGUUCAAGAGCUGAACUGAACACGCUCUAAGAACUGUGCAAAAUAGAUAAGUUGGCUUGUUUGUAAACAAACUUCUCCAACUUUCUAAUUUUGCUUUGUUCUUUACGAGCUUUGUAUCUUGAUU ..........((((((.(((((....((((.....)))))))))..)))))).((((((((...(((((((((.....)))))))))...((((.((((((...((((((((((.(((((((...(((((....)))))....)))))))))).)))))))...))))))...))))...))))).))).. (-62.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 115 75 211 171 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 317 50 5 145 96 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 316 170 142 188 160 smit:SMT_221|5end_prolyl-tRNA_synthetase_153019..153249_POSITIVE 303 160 111 57 3 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 302 48 5 140 97 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 295 168 134 174 142 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 289 171 131 45 6 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 282 166 129 173 132 smit:SMT_1509|5end_phosphopentomutase_1492781..1493011_NEGATIVE 272 160 113 164 115 smit:SMT_1801|5end_heavy_metal_translocating_P-type_ATPase_1773916..1774146_POSITIVE 265 169 122 47 6 smit:SMT_2141|5end_hypothetical_protein_2019976..2020206_NEGATIVE 265 169 122 47 6 smit:SMT_870|5end_hypothetical_protein_818737..818967_NEGATIVE 259 59 17 174 127 smit:SMT_1524|5end_peptidase_T_1504564..1504794_POSITIVE 254 121 90 59 23 smit:SMT_1288|5end_replicative_DNA_helicase_1250854..1251084_POSITIVE 254 50 7 178 132 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 254 50 7 50 4 smit:SMT_545|5end_hypothetical_protein_predicted_by_Glimmer/Critica_461249..461479_POSITIVE 252 168 126 63 20 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 252 184 152 204 176 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 252 120 79 220 181 smit:SMT_824|5end_asparaginyl-tRNA_synthetase_748393..748623_NEGATIVE 251 179 139 57 10 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 250 180 133 71 15 smit:SMT_2049|5end_3-oxoacyl-_1959539..1959769_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 80 31 52 4 smit:SMT_184|3end_30S_ribosomal_protein_S8_121891..122041_POSITIVE 287 116 71 142 96 smit:SMT_558|3end_K09014_Fe-S_cluster_assembly_protein_SufB_476747..476897_POSITIVE 286 111 75 65 29 smit:SMT_1261|3end_MutT/NUDIX_family_protein_1227094..1227244_POSITIVE 282 166 129 149 108 smit:SMT_1510|3end_ribose_5-phosphate_isomerase_1492805..1492955_NEGATIVE 276 170 134 57 12 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 270 124 83 71 29 smit:SMT_1951|3end_ABC_transporter,_ATP-binding_protein_1885141..1885291_NEGATIVE 256 180 151 140 114 smit:SMT_1847|3end_hypothetical_protein_1812697..1812847_POSITIVE 254 50 7 145 99 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 252 184 152 125 97 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 250 180 133 71 15 smit:SMT_2050|3end_K03712_MarR_family_transcriptional_regulator_1959539..1959689_NEGATIVE 243 180 134 53 3 smit:SMT_1971|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903526..1903676_POSITIVE 243 180 134 53 3 smit:SMT_1852|3end_1,4-alpha-glucan_branching_enzyme_1816467..1816617_NEGATIVE 243 180 134 53 3 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE 242 121 82 70 28 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 235 167 134 129 90 smit:SMT_897|3end_serine_O-acetyltransferase_844015..844165_NEGATIVE 235 136 97 109 63 smit:SMT_645|3end_hypothetical_protein_550019..550169_NEGATIVE 234 180 140 48 1 smit:SMT_2024|3end_hypothetical_protein_1940690..1940840_POSITIVE 234 180 140 48 1 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 234 180 140 48 1 smit:SMT_1942|3end_zinc_metalloprotease_ZmpB,_truncated_1878384..1878534_POSITIVE 234 164 135 66 39 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE