Origin IGS: gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt .........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 aaagatgaaagtaatgtataatcagctaatttatctttagagagtagggagcatgtaaatcatttaaaatagtgattccttttgtttaataagagactgtaaaagtattttgacaccttgtcaaagatttcaatttatcggtcctgtttgtgtctattcattcctagaagccgctggcctcatcaatgaccatgaaaatgattgtgactttaatccacataaaaataccgtttgagaaagattc Mask Tandem Repeat Region ================================================ gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt Find is-nt database================================================ Query_seq: SSA_2251:SSA_2252|SSA_2251:SSA_2252:hypothetical protein:hypothetical protein:-><-:2248058..2248301 244 gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2251:SSA_2252|SSA_2251:SSA_2252:hypothetical protein:hypothetical protein:-><-:2248058..2248301 244 gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2251:SSA_2252|SSA_2251:SSA_2252:hypothetical protein:hypothetical protein:-><-:2248058..2248301 244 gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 13 End: 156 ............ V T N K H P N F D C D N E H D N I L G A A E L F S Y V C V P G I F Q F R Q C P T L I S K C D R M ........................................................................................ gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt 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: 120 End: 149 .......................................................................................................................TTTGACAAGGTGTCAAAATACTTTTACAGT............................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2251:SSA_2252|SSA_2251:SSA_2252:hypothetical protein:hypothetical protein:-><-:2248058..2248301 244 gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt Intra-Species Hit: Count: 1 Min: 1 Max: 244 Len: 244 Subject: NC_009009_SSA_2251_SSA_2252|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2248058,2248301]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt gaatctttctcaaacggtatttttatgtggattaaagtcacaatcattttcatggtcattgatgaggccagcggcttctaggaatgaatagacacaaacaggaccgataaattgaaatctttgacaaggtgtcaaaatacttttacagtctcttattaaacaaaaggaatcactattttaaatgatttacatgctccctactctctaaagataaattagctgattatacattactttcatcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUCUUUCUCAAACGGUAUUUUUAUGUGGAUUAAAGUCACAAUCAUUUUCAUGGUCAUUGAUGAGGCCAGCGGCUUCUAGGAAUGAAUAGACACAAACAGGACCGAUAAAUUGAAAUCUUUGACAAGGUGUCAAAAUACUUUUACAGUCUCUUAUUAAACAAAAGGAAUCACUAUUUUAAAUGAUUUACAUGCUCCCUACUCUCUAAAGAUAAAUUAGCUGAUUAUACAUUACUUUCAUCUUU ..((((((.......((((....((((((((((((((..((..(((.(((..(((((.(((..((((((...))))))......((........))..))))))))..))).)))....((((((.....))))))...........))..)))..........((......))........))))))))))).....))))....))))))................................ (-33.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAUGAAAGUAAUGUAUAAUCAGCUAAUUUAUCUUUAGAGAGUAGGGAGCAUGUAAAUCAUUUAAAAUAGUGAUUCCUUUUGUUUAAUAAGAGACUGUAAAAGUAUUUUGACACCUUGUCAAAGAUUUCAAUUUAUCGGUCCUGUUUGUGUCUAUUCAUUCCUAGAAGCCGCUGGCCUCAUCAAUGACCAUGAAAAUGAUUGUGACUUUAAUCCACAUAAAAAUACCGUUUGAGAAAGAUUC (((((((((.....((......)).....)))))))))...((((((.(((((....(((((((......))))))).....)))))....((.((((((((((((.(((((((.....))))))))))....)))).)))))))........))))))....((((......)))).((((..((((..(((....)))..((((.........)))).........))))))))........ (-41.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 80 31 66 29 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 326 85 43 79 30 NC_009009:SSA_1335|5end_Ankyrin_repeat_protein,_putative_1349663..1349893_NEGATIVE 324 108 61 168 111 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 318 100 66 227 195 NC_009009:SSA_0116|5end_30S_ribosomal_protein_S17,_putative_112632..112862_POSITIVE 303 79 35 182 130 NC_009009:SSA_1557|5end_SRPR,_signal_recognition_particle-docking_protein,_putative_1560040..1560270_NEGATIVE 302 78 34 223 171 NC_009009:SSA_2198|5end_hypothetical_protein_2198585..2198815_NEGATIVE 301 86 47 211 174 NC_009009:SSA_0862|5end_MurM,_putative_854221..854451_NEGATIVE 299 106 61 54 9 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 298 86 44 52 4 NC_009009:SSA_0861|5end_hypothetical_protein_852977..853207_NEGATIVE 296 82 51 190 158 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 293 108 63 58 1 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 291 73 33 52 16 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 288 85 47 78 36 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 285 86 50 120 84 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 283 85 49 167 127 NC_009009:SSA_2340|5end_hypothetical_protein_2342843..2343073_NEGATIVE 282 107 66 55 16 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 276 86 44 223 170 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 274 105 66 231 199 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 273 106 61 66 5 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 273 74 41 229 193 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 683 88 41 151 98 NC_009009:SSA_2253|3end_3-Methyladenine_DNA_glycosylase_I,_constitutive,_putative_2248870..2249020_NEGATIVE 322 79 44 136 96 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 312 83 45 139 85 NC_009009:SSA_2199|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2198679..2198829_NEGATIVE 291 73 33 50 14 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 288 107 66 146 101 NC_009009:SSA_2185|3end_Adenylosuccinate_synthetase,_putative_2183998..2184148_NEGATIVE 288 82 41 135 92 NC_009009:SSA_1367|3end_hypothetical_protein_1383828..1383978_POSITIVE 288 85 47 69 27 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 285 86 50 123 87 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 273 110 67 67 30 NC_009009:SSA_0091|3end_V-type_sodium_ATPase,_subunit_A,_putative_92988..93138_POSITIVE 263 74 35 43 1 NC_009009:SSA_1381|3end_hypothetical_protein_1399146..1399296_NEGATIVE 254 81 50 23 1 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 254 110 64 148 99 NC_009009:SSA_0639|3end_hypothetical_protein_627733..627883_NEGATIVE 253 79 43 150 112 NC_009009:SSA_1336|3end_Conserved_ankyrin_repeat_protein,_putative_1349581..1349731_NEGATIVE 251 79 33 145 94 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE 251 110 66 50 13 NC_009009:SSA_0643|3end_hypothetical_protein_630072..630222_NEGATIVE 250 82 44 131 88 NC_009009:SSA_1582|3end_Esterase,_alpha/beta_hydrolase_superfamily,_putative_1585443..1585593_POSITIVE 248 86 54 57 30 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 247 83 50 73 38 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 246 82 59 145 119 NC_009009:SSA_1199|3end_Phosphinothricin_acetyltransferase,_putative_1223311..1223461_NEGATIVE 243 109 63 57 18 NC_009009:SSA_1043|3end_Homoserine_dehydrogenase,_putative_1059931..1060081_POSITIVE