Origin IGS: agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctgaacctccatgattttgattgcttccattatagcacaaaatattatattttcagacaattcttagaatttagcaaaaaaacagaccgaatcgaccgattcaatctgtcttgtatctct Mask Tandem Repeat Region ================================================ agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa Find is-nt database================================================ Query_seq: SSA_0320:SSA_0321|SSA_0320:SSA_0321:hypothetical protein:Methylase, putative:->->:313885..314006 122 agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0320:SSA_0321|SSA_0320:SSA_0321:hypothetical protein:Methylase, putative:->->:313885..314006 122 agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0320:SSA_0321|SSA_0320:SSA_0321:hypothetical protein:Methylase, putative:->->:313885..314006 122 agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 1 End: 120 S I C S L N F R D I R D T K K S F E L F Q R F I Y Y K T S Y H F C D F D H L N M .. agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa 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: 81 Start: 43 End: 72 ..........................................TTTGCTAAATTCTAAGAATTGTCTGAAAAT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0320:SSA_0321|SSA_0320:SSA_0321:hypothetical protein:Methylase, putative:->->:313885..314006 122 agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_009009_SSA_0320_SSA_0321|hypothetical protein:Methylase, putative|POSITIVE:POSITIVE|[313885,314006]|122 HSP 1 e-value: 7.0E-51 bit: 200.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 agagatacaagacagattgaatcggtcgattcggtctgnnnnnnngctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa agagatacaagacagattgaatcggtcgattcggtctgtttttttgctaaattctaagaattgtctgaaaatataatattttgtgctataatggaagcaatcaaaatcatggaggttcagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGAUACAAGACAGAUUGAAUCGGUCGAUUCGGUCUGUUUUUUUGCUAAAUUCUAAGAAUUGUCUGAAAAUAUAAUAUUUUGUGCUAUAAUGGAAGCAAUCAAAAUCAUGGAGGUUCAGAA ..((....(((((((((((((((....)))))))))))))))....))...............((((((..(.....((((((((((........))))..)))))).....)..)))))). (-31.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGAACCUCCAUGAUUUUGAUUGCUUCCAUUAUAGCACAAAAUAUUAUAUUUUCAGACAAUUCUUAGAAUUUAGCAAAAAAACAGACCGAAUCGACCGAUUCAAUCUGUCUUGUAUCUCU .((((((........((((((..((((........))))))))))........))))))................((((....(((((..(((((....)))))..))))).))))...... (-23.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 48 4 54 10 NC_009009:SSA_0332|5end_hypothetical_protein_325909..326139_POSITIVE 295 47 2 43 2 NC_009009:SSA_0594|5end_Transcriptional_regulator,_AraC_family,_putative_585630..585860_POSITIVE 270 43 8 188 154 NC_009009:SSA_1594|5end_Metalloendopeptidase,_putative_1600526..1600756_NEGATIVE 262 37 3 42 3 NC_009009:SSA_2014|5end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014807..2015037_NEGATIVE 259 67 24 179 133 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 253 49 4 156 110 NC_009009:SSA_2120|5end_GTPase,_putative_2121751..2121981_NEGATIVE 249 49 23 227 200 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 246 48 13 61 17 NC_009009:SSA_0412|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_408163..408393_NEGATIVE 245 49 2 198 157 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 245 70 22 78 18 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 245 47 1 55 9 NC_009009:SSA_0121|5end_hypothetical_protein_115183..115413_POSITIVE 244 67 22 184 146 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 242 32 7 41 16 NC_009009:SSA_1549|5end_hypothetical_protein_1552112..1552342_NEGATIVE 239 49 20 123 93 NC_009009:SSA_2068|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_2071311..2071541_NEGATIVE 238 58 12 205 157 NC_009009:SSA_0212|5end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_208373..208603_POSITIVE 237 49 2 71 39 NC_009009:SSA_1775|5end_Potassium_uptake_protein,_Trk_family,_putative_1761284..1761514_POSITIVE 237 59 22 207 167 NC_009009:SSA_1505|5end_hypothetical_protein_1509555..1509785_NEGATIVE 237 49 13 156 119 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 234 50 1 163 111 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 233 67 27 149 109 NC_009009:SSA_1219|5end_Sortase,_putative_1241337..1241567_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 455 42 9 82 49 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE 298 48 3 104 58 NC_009009:SSA_1744|3end_Iron_compound_ABC_transporter,_permease_protein,_putative_1731999..1732149_POSITIVE 296 48 4 57 13 NC_009009:SSA_0331|3end_C3-degrading_proteinase,_putative_325992..326142_POSITIVE 280 44 1 92 45 NC_009009:SSA_0098|3end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_100116..100266_POSITIVE 276 47 1 80 28 NC_009009:SSA_0850|3end_Ubiquitin_C-terminal_hydrolase,_putative_837641..837791_POSITIVE 263 43 1 92 45 NC_009009:SSA_1951|3end_Penicillin-binding_protein_3,_putative_1948103..1948253_POSITIVE 262 37 3 55 16 NC_009009:SSA_2015|3end_Phosphoglycerate_mutase,_putative_2014794..2014944_NEGATIVE 258 48 1 88 33 NC_009009:SSA_1349|3end_Transcriptional_regulator,_biotin_repressor_family,_putative_1366513..1366663_POSITIVE 244 67 22 150 112 NC_009009:SSA_1440|3end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444407..1444557_NEGATIVE 240 45 9 91 58 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 239 49 20 32 2 NC_009009:SSA_2069|3end_Prolyl-tRNA_synthetase,_putative_2071402..2071552_NEGATIVE 234 50 1 121 69 NC_009009:SSA_2012|3end_hypothetical_protein_2012898..2013048_NEGATIVE 233 67 27 134 94 NC_009009:SSA_1220|3end_DNA_gyrase_A_subunit,_putative_1241352..1241502_NEGATIVE 231 55 18 119 84 NC_009009:SSA_1321|3end_Ferrochelatase,_putative_1337246..1337396_NEGATIVE 227 109 65 38 1 NC_009009:SSA_0669|3end_ATP_dependent_protease,_putative_651450..651600_NEGATIVE 227 56 23 98 66 NC_009009:SSA_0426|3end_hypothetical_protein_423565..423715_NEGATIVE 224 50 1 56 14 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 224 39 1 147 108 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 223 66 25 109 71 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 223 48 2 141 79 NC_009009:SSA_1579|3end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1583686..1583836_POSITIVE