Origin IGS: gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc .........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 gaataggctatctatgatgagccttgtaaaactagcgctatgtgattgagaggctgggattatctgtcccggccttttctcacaggattgttagctttttaatatgtttgttacagaaaattatgcaaaaatagtgtaaaataagataaatccttgctgtgtttttggctaaagggattttctcaaattaaaggaatacaaac Mask Tandem Repeat Region ================================================ gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc Find is-nt database================================================ Query_seq: SSA_1408:SSA_1409|SSA_1408:SSA_1409:hypothetical protein:DTDP-glucose-4,6-dehydratase, putative:<-<-:1421096..1421298 203 gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1408:SSA_1409|SSA_1408:SSA_1409:hypothetical protein:DTDP-glucose-4,6-dehydratase, putative:<-<-:1421096..1421298 203 gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1408:SSA_1409|SSA_1408:SSA_1409:hypothetical protein:DTDP-glucose-4,6-dehydratase, putative:<-<-:1421096..1421298 203 gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 26 End: 121 ......................... M P L A K N T A R I Y L I L H Y F C I I F C N K H I K K L T I L .................................................................................. Protein_Len: 30 Strand: - Start: 73 End: 162 ........................................................................ K Q M I K Q L L C I L F S V I R H S F A P V S L G L R E I M ......................................... gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -9.1 Tail_Score: -4.37658 Start: 130 End: 152 Full_Region: gctatgtgattgaga ggctgggat tatct gtcccggcc ttttctcacaggatt .................................................................................................................................ggctgggattatctgtcccggcc................................................... Find igs database================================================ Query_seq: SSA_1408:SSA_1409|SSA_1408:SSA_1409:hypothetical protein:DTDP-glucose-4,6-dehydratase, putative:<-<-:1421096..1421298 203 gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: NC_009009_SSA_1408_SSA_1409|hypothetical protein:DTDP-glucose-4,6-dehydratase, putative|NEGATIVE:NEGATIVE|[1421096,1421298]|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 gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc gtttgtattcctttaatttgagaaaatccctttagccaaaaacacagcaaggatttatcttattttacactatttttgcataattttctgtaacaaacatattaaaaagctaacaatcctgtgagaaaaggccgggacagataatcccagcctctcaatcacatagcgctagttttacaaggctcatcatagatagcctattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUGUAUUCCUUUAAUUUGAGAAAAUCCCUUUAGCCAAAAACACAGCAAGGAUUUAUCUUAUUUUACACUAUUUUUGCAUAAUUUUCUGUAACAAACAUAUUAAAAAGCUAACAAUCCUGUGAGAAAAGGCCGGGACAGAUAAUCCCAGCCUCUCAAUCACAUAGCGCUAGUUUUACAAGGCUCAUCAUAGAUAGCCUAUUC ((((((.......(((..(((((((((((.....((..........))..)))))).)))))..))).........((((........)))))))))).......(((((((.......(((((....((((.((((.......)))).)))).....)))))......)))))))...(((((.(((...)))))))).... (-42.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUAGGCUAUCUAUGAUGAGCCUUGUAAAACUAGCGCUAUGUGAUUGAGAGGCUGGGAUUAUCUGUCCCGGCCUUUUCUCACAGGAUUGUUAGCUUUUUAAUAUGUUUGUUACAGAAAAUUAUGCAAAAAUAGUGUAAAAUAAGAUAAAUCCUUGCUGUGUUUUUGGCUAAAGGGAUUUUCUCAAAUUAAAGGAAUACAAAC ....((((((((...))).)))))((((...((((((...(((((..(((((((((((((.....))))))))))))).)))))....)))))).((((((((.((..............((((((.......))))))....(((.((((((((((((......))))...))))))))))))).))))))))..))))... (-54.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 140 91 231 182 NC_009009:SSA_1408|5end_hypothetical_protein_1421005..1421235_NEGATIVE 365 159 121 216 174 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 317 169 128 44 2 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 316 170 130 197 156 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 315 153 117 177 126 NC_009009:SSA_1519|5end_Polysaccharide/teichoic_acid_transporter,_putative_1526069..1526299_NEGATIVE 308 160 114 151 94 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 302 160 117 72 30 NC_009009:SSA_0427|5end_DNA-binding_transcriptional_activator,_SARP_family,_putative_424497..424727_POSITIVE 301 151 118 200 169 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 301 160 113 80 24 NC_009009:SSA_1004|5end_ABC_transporter_membrane-spanning_permease-multiple_sugars,_putative_1005148..1005378_POSITIVE 299 172 131 117 67 NC_009009:SSA_1449|5end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1451931..1452161_NEGATIVE 299 185 146 52 5 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 298 169 122 100 52 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 294 198 151 55 14 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 292 152 119 65 33 NC_009009:SSA_1634|5end_Heme_utilization/adhesion_exoprotein,_putative_1637062..1637292_NEGATIVE 292 160 129 38 4 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 288 179 132 190 129 NC_009009:SSA_1660|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1657580..1657810_NEGATIVE 288 153 117 131 99 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 288 152 118 73 25 NC_009009:SSA_0991|5end_Deoxyribonuclease,_putative_993342..993572_NEGATIVE 285 160 118 202 144 NC_009009:SSA_2349|5end_DTDP-4-dehydrorhamnose_3,5-epimerase,_putative_2351708..2351938_NEGATIVE 284 190 148 215 170 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 157 115 88 40 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 336 169 121 108 56 NC_009009:SSA_0774|3end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_756075..756225_POSITIVE 329 155 117 73 29 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 318 160 119 96 51 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 309 170 121 88 41 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 307 153 112 85 42 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 302 185 141 59 4 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 301 160 113 66 10 NC_009009:SSA_1003|3end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1005214..1005364_POSITIVE 299 155 120 76 39 NC_009009:SSA_2271|3end_hypothetical_protein_2272238..2272388_NEGATIVE 298 169 122 62 14 NC_009009:SSA_0189|3end_Competence_protein_ComGF,_putative_191523..191673_POSITIVE 295 150 108 135 88 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 293 169 121 149 100 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 292 154 114 135 97 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 288 153 117 83 51 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 280 170 130 68 5 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 278 153 117 91 57 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 278 153 122 85 55 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 277 155 111 136 92 NC_009009:SSA_2062|3end_hypothetical_protein_2063291..2063441_NEGATIVE 272 184 145 92 52 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 272 170 123 151 108 NC_009009:SSA_0365|3end_Small-conductance_mechanosensitive_efflux_channel,_putative_357564..357714_POSITIVE