Origin IGS: catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttataatctcctcgtaattttatattatttcgatttaaggtgaataggttgccattacatttttctcacctctacaaattccaatttgaagcactgtagattatcttcatttcaaatg Mask Tandem Repeat Region ================================================ catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag Find is-nt database================================================ Query_seq: SSA_2385:SSA_1765|SSA_2385:SSA_1765:hypothetical protein:Conserved uncharacterized protein:->->:1753057..1753175 119 catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2385:SSA_1765|SSA_2385:SSA_1765:hypothetical protein:Conserved uncharacterized protein:->->:1753057..1753175 119 catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2385:SSA_1765|SSA_2385:SSA_1765:hypothetical protein:Conserved uncharacterized protein:->->:1753057..1753175 119 catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag Predict ORF larger than 30AA ================================================ catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag 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================================================ catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2385:SSA_1765|SSA_2385:SSA_1765:hypothetical protein:Conserved uncharacterized protein:->->:1753057..1753175 119 catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_009009_SSA_2385_SSA_1765|hypothetical protein:Conserved uncharacterized protein|POSITIVE:POSITIVE|[1753057,1753175]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag catttgaaatgaagataatctacagtgcttcaaattggaatttgtagaggtgagaaaaatgtaatggcaacctattcaccttaaatcgaaataatataaaattacgaggagattataag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUGAAAUGAAGAUAAUCUACAGUGCUUCAAAUUGGAAUUUGUAGAGGUGAGAAAAAUGUAAUGGCAACCUAUUCACCUUAAAUCGAAAUAAUAUAAAAUUACGAGGAGAUUAUAAG ..............(((((((...(((...(((((....)))))..((((((((.....(((....))).....))))))))....................)))....)))))))... (-17.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUAAUCUCCUCGUAAUUUUAUAUUAUUUCGAUUUAAGGUGAAUAGGUUGCCAUUACAUUUUUCUCACCUCUACAAAUUCCAAUUUGAAGCACUGUAGAUUAUCUUCAUUUCAAAUG ...(((((((..(((.(((........))).)))....((((((..(((.((......)).)))..))))))...(((((....))))).........))))))).............. (-13.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 89 44 231 179 NC_009009:SSA_0366|5end_hypothetical_protein_357506..357736_POSITIVE 245 72 34 59 20 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 235 74 37 221 187 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 216 70 22 87 21 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 212 78 34 52 6 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 212 69 28 179 131 NC_009009:SSA_0208|5end_Conserved_uncharacterized_protein_206452..206682_NEGATIVE 209 68 27 199 157 NC_009009:SSA_1638|5end_hypothetical_protein_1641325..1641555_NEGATIVE 206 81 42 47 7 NC_009009:SSA_1400|5end_Pyridoxal_kinase,_putative_1413072..1413302_NEGATIVE 206 50 11 210 166 NC_009009:SSA_1370|5end_CAAX_amino_terminal_protease_family,_putative_1386968..1387198_NEGATIVE 204 69 22 90 39 NC_009009:SSA_1882|5end_Subtilisin-like_serine_proteases,_putative_1880797..1881027_NEGATIVE 204 69 23 119 68 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 204 51 13 120 75 NC_009009:SSA_0425|5end_Glycosyltransferase,_putative_423279..423509_NEGATIVE 202 46 15 150 124 NC_009009:SSA_1212|5end_Ribose-phosphate_pyrophosphokinase_2,_putative_1235401..1235631_POSITIVE 202 80 31 77 31 NC_009009:SSA_0499|5end_ABC-type_dipeptide_transport_system,_periplasmic_component,_putative_498915..499145_POSITIVE 201 72 31 41 5 NC_009009:SSA_1967|5end_Threonine_desaminase,_putative_1963559..1963789_NEGATIVE 200 57 11 198 149 NC_009009:SSA_0138|5end_Metal-binding_(Zn)_permease,_putative_132533..132763_POSITIVE 199 80 44 202 159 NC_009009:SSA_0446|5end_hypothetical_protein_445438..445668_NEGATIVE 196 80 35 108 55 NC_009009:SSA_0152|5end_hypothetical_protein_145799..146029_POSITIVE 191 78 34 229 183 NC_009009:SSA_1009|5end_Galactose-1-phosphate-uridylyltransferase,_putative_1011254..1011484_POSITIVE 190 70 23 198 148 NC_009009:SSA_0351|5end_Signal_peptidase_I,_putative_344907..345137_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 50 18 131 99 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 245 72 34 75 36 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 232 74 37 70 34 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 222 59 15 52 4 NC_009009:SSA_1326|3end_Peptidase_T,_putative_1343735..1343885_POSITIVE 222 52 13 62 19 NC_009009:SSA_0658|3end_Conserved_uncharacterized_protein_642805..642955_POSITIVE 212 78 34 55 9 NC_009009:SSA_0763|3end_Transcription_repressor,_putative_745602..745752_POSITIVE 212 69 28 59 11 NC_009009:SSA_0209|3end_Glutamyl_aminopeptidase,_putative_206572..206722_NEGATIVE 206 50 11 127 83 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 203 110 68 61 19 NC_009009:SSA_1496|3end_hypothetical_protein_1502473..1502623_NEGATIVE 201 83 46 43 10 NC_009009:SSA_0182|3end_Endoglucanase,_putative_187407..187557_POSITIVE 196 80 35 100 47 NC_009009:SSA_0151|3end_hypothetical_protein_145871..146021_POSITIVE 191 47 10 139 111 NC_009009:SSA_0046|3end_Adenylosuccinate_lyase,_putative_52269..52419_POSITIVE 189 82 41 146 104 NC_009009:SSA_1826|3end_Glycerol_kinase,_putative_1816124..1816274_POSITIVE 186 68 26 60 27 NC_009009:SSA_2263|3end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2260688..2260838_NEGATIVE 185 80 44 141 105 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 184 68 26 149 113 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 183 73 32 87 28 NC_009009:SSA_1180|3end_hypothetical_protein_1207819..1207969_NEGATIVE 182 55 11 74 38 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 181 55 14 140 100 NC_009009:SSA_0697|3end_hypothetical_protein_680276..680426_POSITIVE 181 45 7 150 116 NC_009009:SSA_0549|3end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_545651..545801_POSITIVE