Origin IGS: aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatactactatcgccagagcgaacagactctgacctcattttatcatttactctttattttacgataattttgcagaatagtcaaaggttaagggggagaaagtgacaggactt Mask Tandem Repeat Region ================================================ aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Find is-nt database================================================ Query_seq: SMT_377:SMT_378|SMT_377:SMT_378:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:315909..316023 115 aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_377:SMT_378|SMT_377:SMT_378:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:315909..316023 115 aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_377:SMT_378|SMT_377:SMT_378:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:315909..316023 115 aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 12 End: 113 ........... K R G R L R Q S N Q L I I T F Y L T F S L I L D S D T R E P S L L M .. aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa 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: 89 Start: 29 End: 58 ............................TTTGACTATTCTGCAAAATTATCGTAAAAT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_377:SMT_378|SMT_377:SMT_378:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:315909..316023 115 aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: smit_SMT_377_SMT_378|hypothetical protein:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[315909,316023]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa aagtcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Inter-species Hit: Count: 3 Min: 4 Max: 115 Len: 112 Subject: NC_008533_SPD_0440_SPD_0441|hypothetical protein:DNA-directed RNA polymerase, delta subunit, putative|POSITIVE:POSITIVE|[443449,443575]|127 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 112 Query Start:4 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 ...tcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa ...tcctgccactttctcccccttaacctttgactattccgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Subject: NC_003098_spr0436_spr0437|hypothetical protein:DNA-directed RNA polymerase subunit delta|POSITIVE:POSITIVE|[435919,436030]|112 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 112 Query Start:4 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 ...tcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa ...tcctgccactttctcccccttaacctttgactattccgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Subject: NC_003028_SP_0492_SP_0493|hypothetical protein:DNA-directed RNA polymerase subunit delta|POSITIVE:POSITIVE|[469627,469738]|112 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 112 Query Start:4 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 ...tcctgtcactttctcccccttaacctttgactattctgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa ...tcctgccactttctcccccttaacctttgactattccgcaaaattatcgtaaaataaagagtaaatgataaaatgaggtcagagtctgttcgctctggcgatagtagtataa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUGUCACUUUCUCCCCCUUAACCUUUGACUAUUCUGCAAAAUUAUCGUAAAAUAAAGAGUAAAUGAUAAAAUGAGGUCAGAGUCUGUUCGCUCUGGCGAUAGUAGUAUAA ..(((((..........(((((...((((.(......))))).(((((((..............)))))))..))))).((((((......))))))..)))))........ (-19.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUACUACUAUCGCCAGAGCGAACAGACUCUGACCUCAUUUUAUCAUUUACUCUUUAUUUUACGAUAAUUUUGCAGAAUAGUCAAAGGUUAAGGGGGAGAAAGUGACAGGA ...............((((((.....).))))).(((((((((.((.....(((((.(((((..(((.((((....)))).))).))))).))))).)).)))))))..)). (-20.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 110 66 213 161 smit:SMT_543|5end_topoisomerase_IV_subunit_B_458372..458602_POSITIVE 271 102 75 41 14 smit:SMT_414|5end_K03665_GTP-binding_protein_HflX_357554..357784_POSITIVE 262 101 74 200 175 smit:SMT_343|5end_hypothetical_protein_283554..283784_NEGATIVE 261 102 75 44 9 smit:SMT_1170|5end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1118126..1118356_NEGATIVE 259 52 12 42 6 smit:SMT_351|5end_hypothetical_protein_290289..290519_POSITIVE 257 106 73 183 147 smit:SMT_1828|5end_PTS_system,_galactose-specific_IIC_component_1797668..1797898_POSITIVE 257 106 73 83 47 smit:SMT_1827|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1797568..1797798_POSITIVE 251 31 1 125 87 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 247 104 66 224 187 smit:SMT_261|5end_ImpB/MucB/SamB_family_protein_200160..200390_POSITIVE 243 108 78 142 112 smit:SMT_811|5end_ATP-dependent_RNA_helicase_721025..721255_POSITIVE 242 110 73 158 118 smit:SMT_936|5end_cobyric_acid_synthase_888669..888899_POSITIVE 240 107 75 75 40 smit:SMT_673|5end_K01926_AT-rich_DNA-binding_protein_580902..581132_POSITIVE 238 48 14 173 138 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 238 102 81 25 4 smit:SMT_1585|5end_phosphopantetheine_adenylyltransferase_1575242..1575472_POSITIVE 232 42 2 224 174 smit:SMT_1203|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1164394..1164624_NEGATIVE 232 40 5 184 135 smit:SMT_1116|5end_K02244_competence_protein_ComGB_1053841..1054071_NEGATIVE 232 104 70 208 169 smit:SMT_162|5end_hypothetical_protein_106593..106823_POSITIVE 231 49 12 187 150 smit:SMT_976|5end_hypothetical_protein_925183..925413_NEGATIVE 231 108 79 178 141 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 230 102 74 157 124 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 102 75 48 21 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 257 106 73 57 21 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 251 31 1 123 85 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 243 108 78 145 115 smit:SMT_810|3end_oxidoreductase_721108..721258_POSITIVE 238 48 14 117 82 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 238 48 14 117 82 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 238 102 81 35 14 smit:SMT_1584|3end_methyltransferase,_putative_1575332..1575482_POSITIVE 233 109 74 150 107 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 233 104 74 47 13 smit:SMT_998|3end_peptide_chain_release_factor_3_939699..939849_NEGATIVE 232 104 70 121 82 smit:SMT_161|3end_putative_folyl-polyglutamate_synthetase_106586..106736_POSITIVE 231 49 12 118 81 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 231 101 83 46 21 smit:SMT_458|3end_hypothetical_protein_predicted_by_Glimmer/Critica_396729..396879_NEGATIVE 231 96 66 148 110 smit:SMT_398|3end_hypothetical_protein_328279..328429_POSITIVE 230 102 74 138 105 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 229 108 87 116 98 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 228 108 79 147 111 smit:SMT_1073|3end_L-asparaginase_1012251..1012401_POSITIVE 223 48 1 95 36 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 219 100 78 151 130 smit:SMT_344|3end_K02503_Hit-like_protein_involved_in_cell-cycle_regulation_283564..283714_NEGATIVE 217 99 53 81 33 smit:SMT_160|3end_folylpolyglutamate_synthase_105342..105492_POSITIVE 216 108 74 41 13 smit:SMT_1918|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1861816..1861966_NEGATIVE