Origin IGS: ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc .........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 ggcacccgaaagaatatgctactgttgttcttcaagattcatggagagctccttttttcttttattataacatgcaagggagtgggaaacaagactttccaagtagctgaaaaatccttcatctttcaattttgtaagcggttgtgatatactagaaaggaagtttaaaggaaagaaaagcaa Mask Tandem Repeat Region ================================================ ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc Find is-nt database================================================ Query_seq: SSA_2078:SSA_2079|SSA_2078:SSA_2079:hypothetical protein:Acetyltransferase, putative:<-->:2083928..2084110 183 ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2078:SSA_2079|SSA_2078:SSA_2079:hypothetical protein:Acetyltransferase, putative:<-->:2083928..2084110 183 ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2078:SSA_2079|SSA_2078:SSA_2079:hypothetical protein:Acetyltransferase, putative:<-->:2083928..2084110 183 ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 1 End: 162 M L F F P L N F L S S I S Q P L T K L K D E G F F S Y L E S L V S H S L A C Y N K R K K E L S M N L E E Q Q ..................... Protein_Len: 43 Strand: - Start: 40 End: 168 ....................................... L R K C F Q F I F S K E A V Q F T K N G V G K C T I I F S F L L E G H I K F F L L L M ............... ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc 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: 84 Start: 91 End: 120 ..........................................................................................CTTGTTTCCCACTCCCTTGCATGTTATAAT............................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2078:SSA_2079|SSA_2078:SSA_2079:hypothetical protein:Acetyltransferase, putative:<-->:2083928..2084110 183 ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: NC_009009_SSA_2078_SSA_2079|hypothetical protein:Acetyltransferase, putative|NEGATIVE:POSITIVE|[2083928,2084110]|183 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc ttgcttttctttcctttaaacttcctttctagtatatcacaaccgcttacaaaattgaaagatgaaggatttttcagctacttggaaagtcttgtttcccactcccttgcatgttataataaaagaaaaaaggagctctccatgaatcttgaagaacaacagtagcatattctttcgggtgcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUUUUCUUUCCUUUAAACUUCCUUUCUAGUAUAUCACAACCGCUUACAAAAUUGAAAGAUGAAGGAUUUUUCAGCUACUUGGAAAGUCUUGUUUCCCACUCCCUUGCAUGUUAUAAUAAAAGAAAAAAGGAGCUCUCCAUGAAUCUUGAAGAACAACAGUAGCAUAUUCUUUCGGGUGCC ..((...............(((........))).....................((((((((...((((((((((((....))))))))))))..............(((.((((.......((((.....(((....))).....)))).......))))...)))...))))))))..)). (-26.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCACCCGAAAGAAUAUGCUACUGUUGUUCUUCAAGAUUCAUGGAGAGCUCCUUUUUUCUUUUAUUAUAACAUGCAAGGGAGUGGGAAACAAGACUUUCCAAGUAGCUGAAAAAUCCUUCAUCUUUCAAUUUUGUAAGCGGUUGUGAUAUACUAGAAAGGAAGUUUAAAGGAAAGAAAAGCAA ......(....)....((((......((((((((.......))))))))((((((((.....(((((((((.(((..(..(((.(....)...)))..)...(.((.((((......)))).))..)..........))))))))))))....)))))))).................)))). (-39.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 905 110 61 201 152 NC_009009:SSA_2078|5end_hypothetical_protein_2083837..2084067_NEGATIVE 290 46 1 159 113 NC_009009:SSA_2301|5end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2303268..2303498_NEGATIVE 287 140 92 48 3 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 284 140 94 222 171 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 284 110 71 199 151 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 280 46 1 148 93 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 279 39 1 123 82 NC_009009:SSA_0193|5end_CAAX_amino_terminal_protease_family_protein,_putative_194318..194548_POSITIVE 277 110 61 112 53 NC_009009:SSA_1685|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1679076..1679306_NEGATIVE 274 50 2 167 91 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 273 177 134 48 12 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 273 177 134 230 194 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 265 167 123 128 74 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 261 110 80 162 122 NC_009009:SSA_0967|5end_hypothetical_protein_975872..976102_POSITIVE 261 106 61 228 191 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 259 105 69 212 173 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 259 113 82 176 150 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 257 41 2 117 78 NC_009009:SSA_1220|5end_DNA_gyrase_A_subunit,_putative_1243832..1244062_NEGATIVE 255 102 65 121 80 NC_009009:SSA_1362|5end_ORFB,_transposon_ISSsa2_1377911..1378141_POSITIVE 255 179 131 72 15 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 254 110 61 52 6 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 80 31 64 11 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 290 46 1 123 77 NC_009009:SSA_2302|3end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2303304..2303454_NEGATIVE 284 110 71 77 29 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 266 110 69 133 97 NC_009009:SSA_1206|3end_A/G-specific_adenine_glycosylase,_putative_1230071..1230221_NEGATIVE 265 110 67 149 105 NC_009009:SSA_1837|3end_hypothetical_protein_1832955..1833105_POSITIVE 258 178 131 150 98 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE 255 179 131 79 22 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 254 110 61 59 13 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 253 107 66 141 100 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 252 109 70 104 62 NC_009009:SSA_1584|3end_Ring-cleavage_extradiol_dioxygenase,_putative_1586062..1586212_NEGATIVE 252 106 62 55 5 NC_009009:SSA_1031|3end_DNA_topology_modulation_protein_FlaR,_putative_1047734..1047884_NEGATIVE 251 107 70 145 110 NC_009009:SSA_0715|3end_DNA_uptake_protein,_putative_701486..701636_POSITIVE 250 49 2 124 70 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 250 46 3 52 8 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 249 109 62 151 93 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 242 111 76 77 46 NC_009009:SSA_0747|3end_DD-carboxypeptidase,_putative_729371..729521_POSITIVE 234 178 131 140 82 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 233 110 67 140 95 NC_009009:SSA_1789|3end_Metal-dependent_phosphohydrolase,_HD_superfamily,_putative_1772365..1772515_NEGATIVE 233 99 56 55 15 NC_009009:SSA_1086|3end_TRNA_nucleotidyltransferase,_putative_1104607..1104757_POSITIVE 233 115 71 78 28 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE