Origin IGS: aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac .........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 gttttcctccttgaattacaattgatgaaattatagttagctaaacttaattataacttaaatcctctaagttttccacaccttgtggaaaacttagaaaaactgttgataggaattagaaaatacacagattagccgattcccagataaattttacttgttaataaagtgtgaagtatagatgaatatgatagaataaactt Mask Tandem Repeat Region ================================================ aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac Find is-nt database================================================ Query_seq: SSA_2380:SSA_2381|SSA_2380:SSA_2381:hypothetical protein:DegP protein, putative:<-->:2386235..2386437 203 aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2380:SSA_2381|SSA_2380:SSA_2381:hypothetical protein:DegP protein, putative:<-->:2386235..2386437 203 aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2380:SSA_2381|SSA_2380:SSA_2381:hypothetical protein:DegP protein, putative:<-->:2386235..2386437 203 aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac Predict ORF larger than 30AA ================================================ aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac 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: 86 Start: 125 End: 154 ............................................................................................................................GTGGAAAACTTAGAGGATTTAAGTTATAAT................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -17.8 Tail_Score: -3.83154 Start: 103 End: 141 Full_Region: ATTCCTATCAACAGT TTTTCTAAGTTTTCCACA AGG TGTGGAAAACTTAGAGGA TTTAAGTTATAATTA ......................................................................................................TTTTCTAAGTTTTCCACAAGGTGTGGAAAACTTAGAGGA.............................................................. Find igs database================================================ Query_seq: SSA_2380:SSA_2381|SSA_2380:SSA_2381:hypothetical protein:DegP protein, putative:<-->:2386235..2386437 203 aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: NC_009009_SSA_2380_SSA_2381|hypothetical protein:DegP protein, putative|NEGATIVE:POSITIVE|[2386235,2386437]|203 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac aagtttattctatcatattcatctatacttcacactttattaacaagtaaaatttatctgggaatcggctaatctgtgtattttctaattcctatcaacagtttttctaagttttccacaaggtgtggaaaacttagaggatttaagttataattaagtttagctaactataatttcatcaattgtaattcaaggaggaaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUUUAUUCUAUCAUAUUCAUCUAUACUUCACACUUUAUUAACAAGUAAAAUUUAUCUGGGAAUCGGCUAAUCUGUGUAUUUUCUAAUUCCUAUCAACAGUUUUUCUAAGUUUUCCACAAGGUGUGGAAAACUUAGAGGAUUUAAGUUAUAAUUAAGUUUAGCUAACUAUAAUUUCAUCAAUUGUAAUUCAAGGAGGAAAAC ...........................((((..............(((.(((((((..(((((((..(..(((......)))..)..)))))))........(((((((((((((((((.....))))))))))))))))).............))))))).)))...(((((((.....)))))))......))))...... (-40.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUCCUCCUUGAAUUACAAUUGAUGAAAUUAUAGUUAGCUAAACUUAAUUAUAACUUAAAUCCUCUAAGUUUUCCACACCUUGUGGAAAACUUAGAAAAACUGUUGAUAGGAAUUAGAAAAUACACAGAUUAGCCGAUUCCCAGAUAAAUUUUACUUGUUAAUAAAGUGUGAAGUAUAGAUGAAUAUGAUAGAAUAAACUU ...(((.((..((..((((((((((..(..((((((((((......)))))))))).....(((.((((((((((((((.....)))))))))))))).............(((((..(..(((......)))..)..)))))..))).........)..)))))....)))))..))..)).)))................. (-39.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 831 140 91 231 182 NC_009009:SSA_2380|5end_hypothetical_protein_2386144..2386374_NEGATIVE 290 85 58 89 60 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 263 98 55 75 31 NC_009009:SSA_1410|5end_DTDP-4-keto-6-deoxyglucose-3,5-epimerase,_putative_1423086..1423316_NEGATIVE 253 145 105 184 150 NC_009009:SSA_0001|5end_Chromosomal_replication_initiator_protein_dnaA,_putative_74..304_POSITIVE 248 97 58 45 2 NC_009009:SSA_2171|5end_hypothetical_protein_2170760..2170990_NEGATIVE 248 110 65 134 85 NC_009009:SSA_1431|5end_hypothetical_protein_1438730..1438960_NEGATIVE 246 130 81 161 103 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 244 108 66 115 75 NC_009009:SSA_1586|5end_hypothetical_protein_1588182..1588412_NEGATIVE 242 141 113 212 179 NC_009009:SSA_0622|5end_Transcriptional_regulator_(XRE_family),_SOS-response_transcriptional_repressors_(RecA-mediated_autopeptidases),_putative_614419..614649_NEGATIVE 236 86 58 44 15 NC_009009:SSA_1959|5end_Undecaprenyl-diphosphatase,_putative_1956431..1956661_NEGATIVE 236 70 29 78 32 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 234 95 54 131 88 NC_009009:SSA_1697|5end_Tagatose-6-phosphate_kinase,_putative_1690120..1690350_NEGATIVE 229 97 53 121 72 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 227 140 93 69 13 NC_009009:SSA_1970|5end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1966915..1967145_NEGATIVE 225 103 61 45 2 NC_009009:SSA_1958|5end_Adapter_protein_mecA,_putative_1955413..1955643_NEGATIVE 225 128 89 217 175 NC_009009:SSA_0862|5end_MurM,_putative_854221..854451_NEGATIVE 224 93 52 202 162 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 224 107 61 119 69 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 223 126 99 48 20 NC_009009:SSA_2107|5end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2111106..2111336_NEGATIVE 223 70 35 35 1 NC_009009:SSA_0172|5end_Transcriptional_regulator,_XRE_family,_putative_169140..169370_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 98 55 70 26 NC_009009:SSA_1411|3end_Glucose-1-phosphate_thymidylytransferase,_putative_1423091..1423241_NEGATIVE 260 104 68 149 118 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 248 150 101 139 85 NC_009009:SSA_2021|3end_hypothetical_protein_2022500..2022650_NEGATIVE 244 108 66 59 19 NC_009009:SSA_1587|3end_hypothetical_protein_1588238..1588388_NEGATIVE 240 130 81 149 86 NC_009009:SSA_0435|3end_Urocanate_hydratase,_putative_436689..436839_NEGATIVE 234 95 54 118 75 NC_009009:SSA_1698|3end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690133..1690283_NEGATIVE 221 124 81 149 100 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 219 140 91 75 22 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 217 96 61 40 1 NC_009009:SSA_1032|3end_30S_ribosomal_protein_subunit_S20,_putative_1048313..1048463_NEGATIVE 214 129 81 151 102 NC_009009:SSA_0579|3end_Hydrolase,_HAD_superfamily,_putative_572899..573049_POSITIVE 212 95 58 74 38 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 211 97 52 133 93 NC_009009:SSA_1249|3end_hypothetical_protein_1273275..1273425_NEGATIVE 207 150 108 93 49 NC_009009:SSA_1480|3end_hypothetical_protein_1483960..1484110_NEGATIVE 206 130 96 51 14 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 206 130 81 55 7 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 206 153 120 69 29 NC_009009:SSA_0292|3end_Transcriptional_regulator,_AraC_family_(arabinose_operon_control),_putative_287262..287412_POSITIVE 205 138 96 86 40 NC_009009:SSA_2315|3end_Conserved_uncharacterized_protein_2316487..2316637_NEGATIVE 205 109 65 63 19 NC_009009:SSA_2302|3end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2303304..2303454_NEGATIVE 205 120 72 118 68 NC_009009:SSA_2114|3end_Transcriptional_repressor_of_purine_operon,_putative_2116714..2116864_NEGATIVE 205 95 58 113 74 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE