Origin IGS: gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt .........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 aataaaaataccccaaaagttagattttctctgtctaacttttggggtgcagttcaaaaaagcttgatattatgcgttttcttgtgggaagatttactccattttcttcaggaattaagattttgcccagcctcaaaagttctaatcaattttaataactcagaaaaagaagactgacaaaatttaacttaacagacgaaactataaaagttggcgac Mask Tandem Repeat Region ================================================ gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt Find is-nt database================================================ Query_seq: SMT_733:SMT_734|SMT_733:SMT_734:hypothetical protein:hypothetical protein:<-->:639889..640106 218 gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_733:SMT_734|SMT_733:SMT_734:hypothetical protein:hypothetical protein:<-->:639889..640106 218 gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_733:SMT_734|SMT_733:SMT_734:hypothetical protein:hypothetical protein:<-->:639889..640106 218 gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 83 End: 181 .................................................................................. M R L G K I L I P E E N G V N L P T R K R I I S S F F E L H P K S ..................................... Protein_Len: 37 Strand: - Start: 67 End: 177 .................................................................. F Q N S S K L S P L I K I G S S F P T F R G V L F R M I D L K K S S C G M ......................................... Protein_Len: 48 Strand: - Start: 45 End: 188 ............................................ D E K E S N N F N I L V K S A P C F R L E Q L F H L L D E W L F V C L I L S K Q V A G W F N S M .............................. gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt 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================================================ gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_733:SMT_734|SMT_733:SMT_734:hypothetical protein:hypothetical protein:<-->:639889..640106 218 gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt Intra-Species Hit: Count: 1 Min: 1 Max: 218 Len: 218 Subject: smit_SMT_733_SMT_734|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[639889,640106]|218 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 218 Query Start:1 Query End:218 Subject Strand: POSITIVE Subject Start: 1 Subject End: 218 gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt gtcgccaacttttatagtttcgtctgttaagttaaattttgtcagtcttctttttctgagttattaaaattgattagaacttttgaggctgggcaaaatcttaattcctgaagaaaatggagtaaatcttcccacaagaaaacgcataatatcaagcttttttgaactgcaccccaaaagttagacagagaaaatctaacttttggggtatttttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCGCCAACUUUUAUAGUUUCGUCUGUUAAGUUAAAUUUUGUCAGUCUUCUUUUUCUGAGUUAUUAAAAUUGAUUAGAACUUUUGAGGCUGGGCAAAAUCUUAAUUCCUGAAGAAAAUGGAGUAAAUCUUCCCACAAGAAAACGCAUAAUAUCAAGCUUUUUUGAACUGCACCCCAAAAGUUAGACAGAGAAAAUCUAACUUUUGGGGUAUUUUUAUU ...((..(((((.....(((((...((((((....((((((((((((((....((((((.(((.......))))))))).....)))))).))))))))))))))...))))).....)))))...((((.....))))....))......(((((....))))).....(((((((((((((((.........)))))))))))))))......... (-51.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAAAUACCCCAAAAGUUAGAUUUUCUCUGUCUAACUUUUGGGGUGCAGUUCAAAAAAGCUUGAUAUUAUGCGUUUUCUUGUGGGAAGAUUUACUCCAUUUUCUUCAGGAAUUAAGAUUUUGCCCAGCCUCAAAAGUUCUAAUCAAUUUUAAUAACUCAGAAAAAGAAGACUGACAAAAUUUAACUUAACAGACGAAACUAUAAAAGUUGGCGAC ........(((((((((((((((((.......)))))))))))))))))...........(((((.........((((((((((.((((((((.......))))))))))))))...((((((((..(((.((......((((..................)))).....)).))).)))))))).........)))).........)))))...... (-48.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 823 120 71 211 162 smit:SMT_733|5end_hypothetical_protein_639798..640028_NEGATIVE 746 209 162 230 183 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 371 209 163 138 94 smit:SMT_570|5end_hypothetical_protein_488581..488811_POSITIVE 371 209 163 138 94 smit:SMT_542|5end_hypothetical_protein_457940..458170_POSITIVE 285 206 167 221 185 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 280 113 71 62 15 smit:SMT_1173|5end_CMP-N-acetylneuraminate-beta-galactosamide-alpha_-2,3-sialyltransferase_1125620..1125850_NEGATIVE 277 190 144 49 10 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 271 88 41 132 87 smit:SMT_1890|5end_hypothetical_protein_1843407..1843637_POSITIVE 256 44 1 142 98 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 256 170 121 133 84 smit:SMT_408|5end_hypothetical_protein_353087..353317_POSITIVE 249 209 161 188 142 smit:SMT_356|5end_hypothetical_protein_292394..292624_POSITIVE 248 186 144 195 149 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 245 120 71 170 117 smit:SMT_1067|5end_alanine_racemase_1005769..1005999_POSITIVE 244 60 12 143 91 smit:SMT_646|5end_K07284_sortase_A_551702..551932_NEGATIVE 241 210 161 82 24 smit:SMT_972|5end_ABC-type_multidrug/protein/lipid_transport_system,_ATPase_component_920767..920997_NEGATIVE 238 188 144 62 9 smit:SMT_2053|5end_hypothetical_membrane_associated_protein_1964422..1964652_NEGATIVE 236 129 82 71 25 smit:SMT_1332|5end_hypothetical_protein_1307576..1307806_NEGATIVE 233 207 167 194 157 smit:SMT_675|5end_DNA_repair_protein_582977..583207_NEGATIVE 233 130 85 161 122 smit:SMT_341|5end_ThiJ/PfpI_family_protein_280969..281199_POSITIVE 233 139 106 67 35 smit:SMT_205|5end_K02012_iron(III)_transport_system_substrate-binding_protein_137174..137404_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 156 112 95 51 smit:SMT_1018|3end_hypothetical_protein_predicted_by_Glimmer/Critica_954739..954889_POSITIVE 372 189 141 87 37 smit:SMT_735|3end_putative_transposase,_ISSmu1_641395..641545_POSITIVE 351 169 125 45 1 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE 324 210 165 51 3 smit:SMT_1761|3end_transcriptional_activator,_putative_1737185..1737335_POSITIVE 285 206 167 111 75 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 284 187 149 84 46 smit:SMT_571|3end_putative_transposase,_ISSmu1_490009..490159_POSITIVE 282 209 171 63 27 smit:SMT_1313|3end_extramembranal_protein_1278622..1278772_POSITIVE 280 113 71 65 18 smit:SMT_1174|3end_acylneuraminate_cytidylyltransferase_1125617..1125767_NEGATIVE 274 167 127 40 1 smit:SMT_1308|3end_hypothetical_protein_1273854..1274004_POSITIVE 271 88 41 112 67 smit:SMT_1889|3end_hypothetical_protein_1843467..1843617_POSITIVE 256 44 1 140 96 smit:SMT_1693|3end_dimethyladenosine_transferase_1676752..1676902_POSITIVE 256 170 121 132 83 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 256 170 121 132 83 smit:SMT_407|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_353166..353316_POSITIVE 248 170 121 80 31 smit:SMT_1906|3end_peptidyl-tRNA_hydrolase_1853723..1853873_NEGATIVE 244 60 12 143 91 smit:SMT_647|3end_DNA_gyrase,_A_subunit_551702..551852_NEGATIVE 236 129 82 55 9 smit:SMT_1333|3end_glycosyltransferase_1307592..1307742_NEGATIVE 233 135 91 40 3 smit:SMT_1113|3end_hypothetical_protein_1051811..1051961_NEGATIVE 233 207 167 151 114 smit:SMT_676|3end_DNA_helicase_II_583020..583170_NEGATIVE 229 60 16 121 65 smit:SMT_2007|3end_hypothetical_protein_1928147..1928297_POSITIVE 225 46 4 47 11 smit:SMT_1036|3end_alpha-galactosidase_978160..978310_NEGATIVE