Origin IGS: atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacacattcctatctttttgtctgcttactattatactacaaaagctggcacatgggaattttctttatccccaaacaaaaatgccccagcatgagcagggcat Mask Tandem Repeat Region ================================================ atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt Find is-nt database================================================ Query_seq: SMT_144:SMT_145|SMT_144:SMT_145:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:95909..96012 104 atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_144:SMT_145|SMT_144:SMT_145:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:95909..96012 104 atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_144:SMT_145|SMT_144:SMT_145:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:95909..96012 104 atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt Predict ORF larger than 30AA ================================================ atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt 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: 86 Start: 45 End: 74 ............................................ATTCCCATGTGCCAGCTTTTGTAGTATAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_144:SMT_145|SMT_144:SMT_145:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:95909..96012 104 atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: smit_SMT_144_SMT_145|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|POSITIVE:POSITIVE|[95909,96012]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt atgccctgctcatgctggggcatttttgtttggggataaagaaaattcccatgtgccagcttttgtagtataatagtaagcagacaaaaagataggaatgtgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGCCCUGCUCAUGCUGGGGCAUUUUUGUUUGGGGAUAAAGAAAAUUCCCAUGUGCCAGCUUUUGUAGUAUAAUAGUAAGCAGACAAAAAGAUAGGAAUGUGUU .((((((((....)).))))))(((((((((((((((.......))))))).......((((((((......)))).)))).)))))))).............. (-27.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACACAUUCCUAUCUUUUUGUCUGCUUACUAUUAUACUACAAAAGCUGGCACAUGGGAAUUUUCUUUAUCCCCAAACAAAAAUGCCCCAGCAUGAGCAGGGCAU .....((((((((.....((((.((((...............)))).)))).)))))))).....................((((((..((....)).)))))) (-22.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 52 16 83 43 smit:SMT_2167|5end_hypothetical_protein_2039927..2040157_POSITIVE 307 52 16 83 43 smit:SMT_2157|5end_hypothetical_protein_2030615..2030845_POSITIVE 307 52 16 83 43 smit:SMT_1706|5end_hypothetical_protein_1690026..1690256_POSITIVE 307 52 16 83 43 smit:SMT_1546|5end_hypothetical_protein_1530068..1530298_POSITIVE 307 60 11 209 164 smit:SMT_922|5end_RNA-binding_protein_876566..876796_NEGATIVE 305 52 16 83 43 smit:SMT_2172|5end_hypothetical_protein_2043115..2043345_POSITIVE 294 60 12 228 183 smit:SMT_391|5end_PTS_system,_galactose-specific_IIC_component_322647..322877_POSITIVE 284 49 1 83 16 smit:SMT_1008|5end_hypothetical_protein_948021..948251_NEGATIVE 275 60 11 64 13 smit:SMT_1098|5end_hypothetical_protein_1041992..1042222_NEGATIVE 274 43 1 210 152 smit:SMT_1123|5end_hypothetical_protein_1059292..1059522_POSITIVE 266 33 3 88 64 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 255 60 13 191 143 smit:SMT_1461|5end_putative_phosphate_ABC_transporter_(ATP-binding_protein)_1442324..1442554_POSITIVE 252 50 7 59 18 smit:SMT_1668|5end_K+_transport_system,_NAD-binding_component_1658288..1658518_NEGATIVE 251 33 2 118 76 smit:SMT_1808|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1784398..1784628_POSITIVE 251 60 13 70 28 smit:SMT_1431|5end_K08986_putative_membrane_protein_1415759..1415989_POSITIVE 249 68 25 76 20 smit:SMT_1249|5end_hypothetical_protein_1210795..1211025_NEGATIVE 249 42 14 182 156 smit:SMT_1134|5end_glutamyl-tRNA_synthetase_1076464..1076694_NEGATIVE 249 50 1 190 140 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 248 60 13 56 23 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 247 38 6 221 187 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 36 1 146 101 smit:SMT_2042|3end_K04077_chaperonin_GroEL_(Hsp60)_1952960..1953110_NEGATIVE 284 60 11 104 48 smit:SMT_2119|3end_mercuric_reductase_2006145..2006295_POSITIVE 284 60 11 104 48 smit:SMT_1236|3end_mercuric_reductase_1197698..1197848_POSITIVE 277 66 21 82 28 smit:SMT_1328|3end_hypothetical_protein_1304310..1304460_NEGATIVE 252 50 7 45 4 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 251 60 13 73 31 smit:SMT_1430|3end_hypothetical_protein_1415842..1415992_POSITIVE 249 68 25 83 27 smit:SMT_1250|3end_hypothetical_protein_1210788..1210938_NEGATIVE 249 42 14 54 28 smit:SMT_1135|3end_glucose-6-phosphate_isomerase_1076592..1076742_NEGATIVE 243 97 56 61 10 smit:SMT_1046|3end_chaperonin_GroEL_987638..987788_NEGATIVE 241 57 18 65 16 smit:SMT_1499|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483425..1483575_POSITIVE 241 59 12 65 14 smit:SMT_958|3end_hypothetical_protein_predicted_by_Glimmer/Critica_905239..905389_POSITIVE 238 68 26 75 34 smit:SMT_1654|3end_K03110_signal_recognition_particle_receptor_1643519..1643669_POSITIVE 237 59 12 76 25 smit:SMT_2024|3end_hypothetical_protein_1940690..1940840_POSITIVE 237 59 12 65 14 smit:SMT_2002|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1924145..1924295_NEGATIVE 237 59 12 76 25 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 237 59 12 81 30 smit:SMT_1971|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903526..1903676_POSITIVE 237 59 12 65 14 smit:SMT_1966|3end_DNA_polymerase_III_alpha_subunit_1898328..1898478_POSITIVE 237 59 12 76 25 smit:SMT_1942|3end_zinc_metalloprotease_ZmpB,_truncated_1878384..1878534_POSITIVE 237 59 12 65 14 smit:SMT_1927|3end_cell_division_protein_FtsH_1868408..1868558_NEGATIVE 237 59 12 76 25 smit:SMT_1926|3end_mevalonate_kinase_1868062..1868212_POSITIVE