Origin IGS: tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtgtgacctccttaaggtgtattttcccctacacccttatcctaacaaaagaagtacaccaaaccaagctctttttggtaagtggttagattgcgctagtaagtggtagaaaaatcacctaaaaaaga Mask Tandem Repeat Region ================================================ tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac Find is-nt database================================================ Query_seq: SSA_0727:SSA_0728|SSA_0727:SSA_0728:Metal-dependent membrane protease, putative:Protease, putative:->->:713700..713827 128 tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0727:SSA_0728|SSA_0727:SSA_0728:Metal-dependent membrane protease, putative:Protease, putative:->->:713700..713827 128 tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0727:SSA_0728|SSA_0727:SSA_0728:Metal-dependent membrane protease, putative:Protease, putative:->->:713700..713827 128 tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 23 End: 112 ...................... W K S A C D L W K G F L A Q N P T S R K N P Y P H L P F Y M ................ tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac 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================================================ tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0727:SSA_0728|SSA_0727:SSA_0728:Metal-dependent membrane protease, putative:Protease, putative:->->:713700..713827 128 tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_009009_SSA_0727_SSA_0728|Metal-dependent membrane protease, putative:Protease, putative|POSITIVE:POSITIVE|[713700,713827]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac tcttttttaggtgatttttctaccacttactagcgcaatctaaccacttaccaaaaagagcttggtttggtgtacttcttttgttaggataagggtgtaggggaaaatacaccttaaggaggtcacac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUUUAGGUGAUUUUUCUACCACUUACUAGCGCAAUCUAACCACUUACCAAAAAGAGCUUGGUUUGGUGUACUUCUUUUGUUAGGAUAAGGGUGUAGGGGAAAAUACACCUUAAGGAGGUCACAC (((((((.((((((((((((((((.((((((((((.........((((.(((((.......)))))..)))).........))))))..)))))))....)))))))).))))).)))))))...... (-34.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUGACCUCCUUAAGGUGUAUUUUCCCCUACACCCUUAUCCUAACAAAAGAAGUACACCAAACCAAGCUCUUUUUGGUAAGUGGUUAGAUUGCGCUAGUAAGUGGUAGAAAAAUCACCUAAAAAAGA ..............(((((..(((((..((((.........................((((.((((((.....))))))...))))....((((....))))))))..)))))..)))))........ (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 64 22 56 11 NC_009009:SSA_0715|5end_DNA_uptake_protein,_putative_700726..700956_POSITIVE 294 48 1 150 101 NC_009009:SSA_1146|5end_Phosphotransferase_system_cellobiose-specific_component_IIA,_putative_1176453..1176683_POSITIVE 281 98 57 130 81 NC_009009:SSA_1678|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1672181..1672411_NEGATIVE 277 95 51 174 129 NC_009009:SSA_1772|5end_hypothetical_protein_1759545..1759775_NEGATIVE 264 104 61 217 166 NC_009009:SSA_1505|5end_hypothetical_protein_1509555..1509785_NEGATIVE 264 80 31 87 27 NC_009009:SSA_1267|5end_crcB-like_protein_2,_putative_1291347..1291577_NEGATIVE 259 75 35 160 117 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 256 102 61 216 178 NC_009009:SSA_2171|5end_hypothetical_protein_2170760..2170990_NEGATIVE 256 110 61 182 142 NC_009009:SSA_0454|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_457015..457245_NEGATIVE 255 70 23 56 9 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 253 98 55 175 128 NC_009009:SSA_1130|5end_Iron-dependent_peroxidase,_putative_1155802..1156032_POSITIVE 252 89 47 176 140 NC_009009:SSA_1514|5end_Cell-wall_biogenesis_glycosyltransferase,_putative_1521780..1522010_NEGATIVE 252 100 60 54 11 NC_009009:SSA_1262|5end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1287782..1288012_POSITIVE 252 89 44 68 19 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 252 80 31 88 25 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 252 70 23 66 27 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 248 105 63 140 91 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 248 89 43 211 160 NC_009009:SSA_1641|5end_MutT/nudix_family_protein,_putative_1643094..1643324_NEGATIVE 247 99 59 100 44 NC_009009:SSA_0182|5end_Endoglucanase,_putative_186299..186529_POSITIVE 238 116 73 156 95 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 95 55 103 64 NC_009009:SSA_1710|3end_Transcriptional_regulator,_XRE_family,_putative_1699011..1699161_POSITIVE 281 98 57 128 79 NC_009009:SSA_1679|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1672183..1672333_NEGATIVE 275 105 64 82 34 NC_009009:SSA_1246|3end_hypothetical_protein_1269798..1269948_NEGATIVE 264 80 31 87 27 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 261 70 26 117 63 NC_009009:SSA_1503|3end_Ferredoxin,_putative_1506492..1506642_POSITIVE 253 83 57 150 118 NC_009009:SSA_1185|3end_DNA_processing_Smf_protein,_putative_1213690..1213840_NEGATIVE 252 80 31 98 35 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 248 78 42 42 5 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 246 71 35 147 113 NC_009009:SSA_1075|3end_Coproporphyrinogen_III_oxidase,_putative_1094303..1094453_POSITIVE 238 84 53 85 50 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 234 94 55 40 4 NC_009009:SSA_1658|3end_Cationic_amino_acid_transporter,_putative_1653274..1653424_NEGATIVE 232 103 72 145 107 NC_009009:SSA_1171|3end_Tyrosine_recombinase_xerC_1199238..1199388_POSITIVE 229 98 57 140 95 NC_009009:SSA_0813|3end_Thioredoxin_reductase,_putative_794438..794588_NEGATIVE 229 71 32 87 47 NC_009009:SSA_0636|3end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625809..625959_POSITIVE 229 100 56 151 116 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 228 90 51 78 44 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 225 104 64 121 78 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 225 46 2 97 36 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 224 98 51 111 70 NC_009009:SSA_1563|3end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1566456..1566606_NEGATIVE 223 48 4 139 105 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE