Origin IGS: tctccctcccttcacttctttcctgctatcctttcttttattttatcatatatttatatagattttaatcgctaacattcttttgaaaaatactttttttgctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgaaacctcctgaaattttcttactataattgtaaaccttttcactatagaagtaaagcaaaaaaagtatttttcaaaagaatgttagcgattaaaatctatataaatatatgataaaataaaagaaaggatagcaggaaagaagtgaagggagggaga Mask Tandem Repeat Region ================================================ tctccctcccttcacttctttcctgctatcctttcttttattttatcatatatttatatagattttaatcgctaacattcttttgaaaaatactttttttgctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt Find is-nt database================================================ Query_seq: SMT_1070:SMT_1071|SMT_1070:SMT_1071:hypothetical protein:hypothetical protein:<-->:1010037..1010197 161 tctccctcccttcacttctttcctgctatcctttcttttattttatcatatatttatatagattttaatcgctaacattcttttgaaaaatactttttttgctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1070:SMT_1071|SMT_1070:SMT_1071:hypothetical protein:hypothetical protein:<-->:1010037..1010197 161 tctccctcccttcacttctttcctgctatcctttcttttattttatcatatatttatatagattttaatcgctaacattcttttgaaaaatactttttttgctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1070:SMT_1071|SMT_1070:SMT_1071:hypothetical protein:hypothetical protein:<-->:1010037..1010197 161 tctccctcccttcacttctttcctgctatcctttcttttattttatcatatatttatatagattttaatcgctaacattcttttgaaaaatactttttttgctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctccctcccttcacttctttcctgctatcctttcttttattttatcatatatttatatagattttaatcgctaacattcttttgaaaaatactttttttgctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 49 End: 150 ................................................ I N I Y I K I A L M R K F F V K K A K S R Y H F P K C N Y Y S F K M ........... tctccctcccttcacttctttcctgctatcctttcttttattttatcatatatttatatagattttaatcgctaacattcttttgaaaaatactttttttgctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt 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: 83 Start: 40 End: 69 .......................................ATTAAAATCTATATAAATATATGATAAAAT............................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 102 End: 131 .....................................................................................................CTTTACTTCTATAGTGAAAAGGTTTACAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctccctcccttcacttctttcctgctatcctttcttttattttatcatatatttatatagattttaatcgctaacattcttttgaaaaatactttttttgctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1070:SMT_1071|SMT_1070:SMT_1071:hypothetical protein:hypothetical protein:<-->:1010037..1010197 161 tctccctcccttcacttctttcctgctatcctttcttttattttatcatatatttatatagattttaatcgctaacattcttttgaaaaatactttttttgctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: smit_SMT_1070_SMT_1071|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1010037,1010197]|161 HSP 1 e-value: 7.0E-27 bit: 121.0 Len: 61 Query Start:101 Query End:161 Subject Strand: POSITIVE Subject Start: 101 Subject End: 161 ....................................................................................................gctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt ....................................................................................................gctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt HSP 2 e-value: 2.0E-11 bit: 69.9 Len: 35 Query Start:1 Query End:35 Subject Strand: POSITIVE Subject Start: 1 Subject End: 35 tctccctcccttcacttctttcctgctatcctttc.............................................................................................................................. tctccctcccttcacttctttcctgctatcctttc.............................................................................................................................. Inter-species Hit: Count: 2 Min: 1 Max: 161 Len: 161 Subject: NC_008533_SPD_1792_SPD_1793|hypothetical protein:universal stress protein family protein|NEGATIVE:POSITIVE|[1787543,1787703]|161 HSP 1 e-value: 7.0E-27 bit: 121.0 Len: 61 Query Start:101 Query End:161 Subject Strand: POSITIVE Subject Start: 101 Subject End: 161 ....................................................................................................gctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt ....................................................................................................gctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt HSP 2 e-value: 6.0E-9 bit: 61.9 Len: 35 Query Start:1 Query End:35 Subject Strand: POSITIVE Subject Start: 1 Subject End: 35 tctccctcccttcacttctttcctgctatcctttc.............................................................................................................................. tctcccttccttcacttctttcctgctatcctttc.............................................................................................................................. Subject: NC_003028_SP_1995_SP_1996|hypothetical protein:universal stress protein family|NEGATIVE:POSITIVE|[1898594,1898754]|161 HSP 1 e-value: 7.0E-27 bit: 121.0 Len: 61 Query Start:101 Query End:161 Subject Strand: POSITIVE Subject Start: 101 Subject End: 161 ....................................................................................................gctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt ....................................................................................................gctttacttctatagtgaaaaggtttacaattatagtaagaaaatttcaggaggtttcatt HSP 2 e-value: 6.0E-9 bit: 61.9 Len: 35 Query Start:1 Query End:35 Subject Strand: POSITIVE Subject Start: 1 Subject End: 35 tctccctcccttcacttctttcctgctatcctttc.............................................................................................................................. tctcccttccttcacttctttcctgctatcctttc.............................................................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCCCUCCCUUCACUUCUUUCCUGCUAUCCUUUCUUUUAUUUUAUCAUAUAUUUAUAUAGAUUUUAAUCGCUAACAUUCUUUUGAAAAAUACUUUUUUUGCUUUACUUCUAUAGUGAAAAGGUUUACAAUUAUAGUAAGAAAAUUUCAGGAGGUUUCAUU ....(((((.........((((.((((((.........((((((.(((............(((....))).............))))))))).((((((..((.((....)).))..)))))).........)))))).))))......)))))....... (-19.67) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAAACCUCCUGAAAUUUUCUUACUAUAAUUGUAAACCUUUUCACUAUAGAAGUAAAGCAAAAAAAGUAUUUUUCAAAAGAAUGUUAGCGAUUAAAAUCUAUAUAAAUAUAUGAUAAAAUAAAAGAAAGGAUAGCAGGAAAGAAGUGAAGGGAGGGAGA .......((((((.....((((((.((.(((((((.(((...(((.....(((((((............))))))).....))).))).)))))))..(((((((....)))).))).....................)).))))))....)))))).... (-24.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 836 50 1 141 92 smit:SMT_1070|5end_hypothetical_protein_1009946..1010176_NEGATIVE 345 32 1 110 79 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 287 33 5 140 110 smit:SMT_659|5end_hypothetical_protein_570545..570775_NEGATIVE 280 46 10 138 97 smit:SMT_359|5end_transcription_termination-antitermination_factor_294470..294700_POSITIVE 276 36 1 227 190 smit:SMT_434|5end_orotidine_5'-phosphate_decarboxylase_376107..376337_POSITIVE 270 51 16 133 95 smit:SMT_1639|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1625819..1626049_NEGATIVE 260 51 20 123 96 smit:SMT_1344|5end_oligoendopeptidase_F_1322798..1323028_NEGATIVE 254 39 3 147 97 smit:SMT_478|5end_hypothetical_protein_predicted_by_Glimmer/Critica_414644..414874_POSITIVE 247 48 2 150 98 smit:SMT_628|5end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_532831..533061_POSITIVE 247 50 3 92 34 smit:SMT_227|5end_hypothetical_protein_164039..164269_POSITIVE 247 50 3 92 34 smit:SMT_224|5end_hypothetical_protein_158470..158700_POSITIVE 241 40 6 65 26 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 237 49 11 115 71 smit:SMT_558|5end_K09014_Fe-S_cluster_assembly_protein_SufB_475255..475485_POSITIVE 235 31 8 122 97 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 234 31 5 69 43 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 234 43 9 53 21 smit:SMT_1333|5end_glycosyltransferase_1308635..1308865_NEGATIVE 230 26 3 222 198 smit:SMT_990|5end_hypothetical_protein_933947..934177_NEGATIVE 230 36 3 201 162 smit:SMT_895|5end_cysteinyl-tRNA_synthetase_843037..843267_NEGATIVE 229 149 105 218 169 smit:SMT_117|5end_K02025_multiple_sugar_transport_system_permease_protein_68487..68717_POSITIVE 227 34 9 117 95 smit:SMT_522|5end_K02003_446719..446949_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 33 5 147 117 smit:SMT_660|3end_two-component_sensor_histidine_kinase_570538..570688_NEGATIVE 280 46 10 94 53 smit:SMT_358|3end_hypothetical_protein_294506..294656_POSITIVE 260 51 20 104 77 smit:SMT_1345|3end_K06198_competence_protein_CoiA_1322817..1322967_NEGATIVE 237 49 11 57 13 smit:SMT_557|3end_K04488_nitrogen_fixation_protein_NifU_and_related_proteins_475277..475427_POSITIVE 235 31 8 120 95 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 230 26 3 136 112 smit:SMT_991|3end_hypothetical_protein_934033..934183_NEGATIVE 230 36 3 119 80 smit:SMT_896|3end_hypothetical_protein_843119..843269_NEGATIVE 230 48 1 66 9 smit:SMT_693|3end_hypothetical_protein_604078..604228_POSITIVE 227 34 9 133 111 smit:SMT_521|3end_K02005_HlyD_family_secretion_protein_446815..446965_POSITIVE 224 43 10 49 14 smit:SMT_1548|3end_cell_division_protein_FtsZ_1533720..1533870_POSITIVE 224 31 1 136 89 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 224 31 10 139 119 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 223 46 2 94 42 smit:SMT_1704|3end_D-alanine-D-alanine_ligase_1688554..1688704_POSITIVE 220 48 18 51 24 smit:SMT_1930|3end_peptide_chain_release_factor_1_1869785..1869935_NEGATIVE 220 48 18 146 119 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 220 50 7 45 1 smit:SMT_1375|3end_putative_glucose-inhibited_division_protein_1353104..1353254_NEGATIVE 216 44 7 54 15 smit:SMT_978|3end_hypothetical_protein_925765..925915_NEGATIVE 209 50 3 52 7 smit:SMT_1736|3end_acetyltransferase,_GNAT_family_1719862..1720012_POSITIVE 209 62 21 67 27 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 205 37 3 144 111 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE