Origin IGS: tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttagaataaataatgatattttcaaaaatattgcataaaaatacataaaatacttgacaaagggaaaatatgcgagtaaaataaaacgcatatttatacggaggtgttttaaaaat .........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 atttttaaaacacctccgtataaatatgcgttttattttactcgcatattttccctttgtcaagtattttatgtatttttatgcaatatttttgaaaatatcattatttattctaaaacaattcatactttcttgccgaaaaacggcctatttgcttctcatatagagaagtaaaggagctgagagcacagaaaaagatccgcccaaagagcagaccttttcatctatctgttatctaata Mask Tandem Repeat Region ================================================ tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttagaataaataatgatattttcaaaaatattgcataaaaatacataaaatacttgacaaagggaaaatatgcgagtaaaataaaacgcatatttatacggaggtgttttaaaaat Find is-nt database================================================ Query_seq: SSA_0756:SSA_0757|SSA_0756:SSA_0757:Alanyl-tRNA synthetase, putative:N-acetyl-gamma-glutamyl-phosphate reductase, putative:->->:739495..739735 241 tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttagaataaataatgatattttcaaaaatattgcataaaaatacataaaatacttgacaaagggaaaatatgcgagtaaaataaaacgcatatttatacggaggtgttttaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0756:SSA_0757|SSA_0756:SSA_0757:Alanyl-tRNA synthetase, putative:N-acetyl-gamma-glutamyl-phosphate reductase, putative:->->:739495..739735 241 tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttagaataaataatgatattttcaaaaatattgcataaaaatacataaaatacttgacaaagggaaaatatgcgagtaaaataaaacgcatatttatacggaggtgttttaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0756:SSA_0757|SSA_0756:SSA_0757:Alanyl-tRNA synthetase, putative:N-acetyl-gamma-glutamyl-phosphate reductase, putative:->->:739495..739735 241 tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttagaataaataatgatattttcaaaaatattgcataaaaatacataaaatacttgacaaagggaaaatatgcgagtaaaataaaacgcatatttatacggaggtgttttaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttagaataaataatgatattttcaaaaatattgcataaaaatacataaaatacttgacaaagggaaaatatgcgagtaaaataaaacgcatatttatacggaggtgttttaaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 28 End: 126 ........................... M L F G R I F F C A L S S F T S L Y E K Q I G R F S A R K Y E L F ................................................................................................................... Protein_Len: 48 Strand: - Start: 79 End: 222 .............................................................................. I L L L Y A T K R C S L I F Q K L I F L S I K L F I A Y F Y M F Y K V F P F Y A L L I F R M N M ................... Protein_Len: 57 Strand: - Start: 71 End: 241 ...................................................................... K E I H S A F L G N K P L F T H I T K S Y I I I N E F I N C L F V Y F V Q C L S F I R T F Y F A Y K Y P P T K F M Protein_Len: 30 Strand: - Start: 6 End: 92 ..... * I V S L H F P R S K P R I K K Q A R L E K V E R Y S F C M ..................................................................................................................................................... tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttagaataaataatgatattttcaaaaatattgcataaaaatacataaaatacttgacaaagggaaaatatgcgagtaaaataaaacgcatatttatacggaggtgttttaaaaat 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: 88 Start: 178 End: 207 .................................................................................................................................................................................CTTGACAAAGGGAAAATATGCGAGTAAAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttagaataaataatgatattttcaaaaatattgcataaaaatacataaaatacttgacaaagggaaaatatgcgagtaaaataaaacgcatatttatacggaggtgttttaaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0756:SSA_0757|SSA_0756:SSA_0757:Alanyl-tRNA synthetase, putative:N-acetyl-gamma-glutamyl-phosphate reductase, putative:->->:739495..739735 241 tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttagaataaataatgatattttcaaaaatattgcataaaaatacataaaatacttgacaaagggaaaatatgcgagtaaaataaaacgcatatttatacggaggtgttttaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 241 Len: 241 Subject: NC_009009_SSA_0756_SSA_0757|Alanyl-tRNA synthetase, putative:N-acetyl-gamma-glutamyl-phosphate reductase, putative|POSITIVE:POSITIVE|[739495,739735]|241 HSP 1 e-value: 3.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttag................................................................................................................ tattagataacagatagatgaaaaggtctgctctttgggcggatctttttctgtgctctcagctcctttacttctctatatgagaagcaaataggccgtttttcggcaagaaagtatgaattgttttag................................................................................................................ HSP 2 e-value: 4.0E-8 bit: 60.0 Len: 30 Query Start:212 Query End:241 Subject Strand: POSITIVE Subject Start: 212 Subject End: 241 ...................................................................................................................................................................................................................cgcatatttatacggaggtgttttaaaaat ...................................................................................................................................................................................................................cgcatatttatacggaggtgttttaaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAGAUAACAGAUAGAUGAAAAGGUCUGCUCUUUGGGCGGAUCUUUUUCUGUGCUCUCAGCUCCUUUACUUCUCUAUAUGAGAAGCAAAUAGGCCGUUUUUCGGCAAGAAAGUAUGAAUUGUUUUAGAAUAAAUAAUGAUAUUUUCAAAAAUAUUGCAUAAAAAUACAUAAAAUACUUGACAAAGGGAAAAUAUGCGAGUAAAAUAAAACGCAUAUUUAUACGGAGGUGUUUUAAAAAU ....(((..(((((......((((((((((((.....)))))))))))))))))..)))((.((((......((((.....)))).((((....((((.....))))..((((((((..(((((((......))))))).)))))))).......))))..................(((....)))...(((((((((............)))))))))....)))).)).......... (-61.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUAAAACACCUCCGUAUAAAUAUGCGUUUUAUUUUACUCGCAUAUUUUCCCUUUGUCAAGUAUUUUAUGUAUUUUUAUGCAAUAUUUUUGAAAAUAUCAUUAUUUAUUCUAAAACAAUUCAUACUUUCUUGCCGAAAAACGGCCUAUUUGCUUCUCAUAUAGAGAAGUAAAGGAGCUGAGAGCACAGAAAAAGAUCCGCCCAAAGAGCAGACCUUUUCAUCUAUCUGUUAUCUAAUA ..........((.((((....(((((((((............)))))))))..........((((((....(((((....)))))..........(((((....)))))...............))))))....((((.....))))...((((((((((.....)))))))))))))).)).((..((((((((((.((.((.......)).)).)))))......)))))..))..... (-45.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 73 33 110 66 NC_009009:SSA_1028|5end_Transcriptional_repressor,_XRE_family,_putative_1046063..1046293_NEGATIVE 346 69 22 56 12 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 331 69 24 205 160 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 326 65 23 74 20 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 322 66 23 181 137 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 316 98 51 122 73 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 309 63 22 62 26 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 305 70 24 202 145 NC_009009:SSA_2223|5end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224703..2224933_NEGATIVE 305 68 24 67 27 NC_009009:SSA_0761|5end_Transcriptional_regulator,_XRE_family,_putative_743877..744107_POSITIVE 301 59 15 147 107 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 298 68 25 204 168 NC_009009:SSA_1508|5end_ABC-type_lipopolysaccharide_transport_system,_permease_component,_putative_1513250..1513480_NEGATIVE 295 57 11 84 35 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 295 76 36 109 62 NC_009009:SSA_0899|5end_Conserved_permease,_putative_889903..890133_POSITIVE 294 68 25 163 122 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 294 67 25 151 95 NC_009009:SSA_1764|5end_hypothetical_protein_1750868..1751098_POSITIVE 294 66 22 231 183 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 294 57 13 60 5 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 293 66 23 195 146 NC_009009:SSA_2140|5end_Ribonuclease_P_protein_component,_putative_2140574..2140804_NEGATIVE 292 76 31 209 157 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 292 63 25 60 17 NC_009009:SSA_0837|5end_Glucosyltransferase,_putative_823902..824132_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 59 12 86 34 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 332 57 15 107 62 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 331 69 24 83 38 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 326 58 12 97 53 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 326 65 23 81 27 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 324 65 27 113 55 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 316 98 51 69 20 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 312 77 36 89 43 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 310 67 23 119 66 NC_009009:SSA_0596|3end_hypothetical_protein_587352..587502_POSITIVE 309 63 22 84 48 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 303 55 14 90 53 NC_009009:SSA_2329|3end_hypothetical_protein_2333169..2333319_POSITIVE 298 67 25 70 24 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 293 60 19 60 9 NC_009009:SSA_2378|3end_Two-component_system_transcriptional_regulator,_LytR/AlgR_family,_putative_2383129..2383279_NEGATIVE 293 65 25 150 98 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 292 63 25 47 4 NC_009009:SSA_0836|3end_SecA-like_protein,_putative_823969..824119_POSITIVE 290 70 26 127 72 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 288 55 12 75 33 NC_009009:SSA_0697|3end_hypothetical_protein_680276..680426_POSITIVE 287 50 13 91 54 NC_009009:SSA_2330|3end_Acetyltransferase,_putative_2333170..2333320_NEGATIVE 287 100 51 107 53 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 286 69 21 119 57 NC_009009:SSA_1111|3end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1137940..1138090_POSITIVE