Origin IGS: cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttctagcctccttgtgcataataataagttactattattatatcatgaatacagtaaaaaaatacttttgaaaagtattctcgttaaattagaaattggctgactgcgctaaatctgcataaaaattatcaaaagtttttaaattactg Mask Tandem Repeat Region ================================================ cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag Find is-nt database================================================ Query_seq: SSA_0968:SSA_0969|SSA_0968:SSA_0969:hypothetical protein:hypothetical protein:->->:977202..977351 150 cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0968:SSA_0969|SSA_0968:SSA_0969:hypothetical protein:hypothetical protein:->->:977202..977351 150 cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0968:SSA_0969|SSA_0968:SSA_0969:hypothetical protein:hypothetical protein:->->:977202..977351 150 cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag Predict ORF larger than 30AA ================================================ cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag 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================================================ cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -5.8 Tail_Score: -5.62219 Start: 73 End: 87 Full_Region: CTAATTTAACGAGAA TACTTT TCA AAAGTA TTTTTTTACTGTATT ........................................................................TACTTTTCAAAAGTA............................................................... Find igs database================================================ Query_seq: SSA_0968:SSA_0969|SSA_0968:SSA_0969:hypothetical protein:hypothetical protein:->->:977202..977351 150 cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag Intra-Species Hit: Count: 2 Min: 1 Max: 150 Len: 150 Subject: NC_009009_SSA_0968_SSA_0969|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[977202,977351]|150 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtannnnnnnactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag cagtaatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaacttattattatgcacaaggaggctagaag Subject: NC_009009_SSA_0969_SSA_0970|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[977790,977929]|140 HSP 1 e-value: 5.0E-31 bit: 135.0 Len: 121 Query Start:4 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 ...taatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtannnnnnnactgtattcatgatataataatagtaactt.......................... ...taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaactt.......................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUAAUUUAAAAACUUUUGAUAAUUUUUAUGCAGAUUUAGCGCAGUCAGCCAAUUUCUAAUUUAACGAGAAUACUUUUCAAAAGUAUUUUUUUACUGUAUUCAUGAUAUAAUAAUAGUAACUUAUUAUUAUGCACAAGGAGGCUAGAAG ((((((...(((.((((((((..........((.((((......)))).))...((((.........)))).......)))))))).)))..))))))..(((.((.(((((((((((....)))))))))))..)).)))......... (-23.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUAGCCUCCUUGUGCAUAAUAAUAAGUUACUAUUAUUAUAUCAUGAAUACAGUAAAAAAAUACUUUUGAAAAGUAUUCUCGUUAAAUUAGAAAUUGGCUGACUGCGCUAAAUCUGCAUAAAAAUUAUCAAAAGUUUUUAAAUUACUG ............(..((.(((((((((......)))))))))..))..)...((((((..(((.((((((((...(((.((..(((((........))))).)).)))((.......))..........)))))))).)))...)))))) (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 78 32 59 15 NC_009009:SSA_1936|5end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923838..1924068_NEGATIVE 291 72 32 160 124 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 286 52 23 50 14 NC_009009:SSA_1930|5end_Acetyl-CoA_carboxylase_alpha_subunit,_putative_1918547..1918777_NEGATIVE 270 79 33 156 118 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 251 69 28 172 137 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 248 53 31 76 53 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 242 59 20 180 133 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 242 86 45 198 146 NC_009009:SSA_0627|5end_hypothetical_protein_617314..617544_POSITIVE 236 80 33 212 159 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 236 59 32 152 124 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 235 74 45 182 144 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 234 65 32 77 46 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 232 67 26 148 111 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 230 73 33 45 14 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 227 54 15 49 17 NC_009009:SSA_1629|5end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1630338..1630568_POSITIVE 226 108 67 94 50 NC_009009:SSA_1487|5end_Conserved_uncharacterized_protein_1494190..1494420_NEGATIVE 224 74 34 69 39 NC_009009:SSA_1792|5end_Preprotein_translocase_subunit_YidC,_putative_1774036..1774266_POSITIVE 224 77 31 182 141 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 220 59 16 173 119 NC_009009:SSA_0980|5end_3-isopropylmalate_dehydratase_large_subunit,_putative_984004..984234_POSITIVE 220 67 24 181 134 NC_009009:SSA_0934|5end_HydD,_putative_943208..943438_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 78 32 46 2 NC_009009:SSA_1937|3end_Malonyl-CoA:ACP_transacylase,_putative_1923851..1924001_NEGATIVE 291 72 32 144 108 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 286 52 23 53 17 NC_009009:SSA_1931|3end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta,_putative_1918544..1918694_NEGATIVE 240 58 33 147 121 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 235 74 45 131 93 NC_009009:SSA_1904|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1898233..1898383_NEGATIVE 234 65 32 93 62 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 234 70 21 149 93 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 232 55 20 147 108 NC_009009:SSA_2240|3end_Holliday_junction_resolvase,_putative_2237258..2237408_NEGATIVE 230 73 33 48 17 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 227 53 15 140 99 NC_009009:SSA_1063|3end_Peptidoglycan-binding_domain-containing_protein,_putative_1080260..1080410_POSITIVE 226 108 67 76 32 NC_009009:SSA_1488|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_1494208..1494358_NEGATIVE 220 67 24 150 103 NC_009009:SSA_0933|3end_Acetyltransferase,_GNAT_family,_putative_943257..943407_POSITIVE 219 79 32 44 2 NC_009009:SSA_0835|3end_Accessory_secretory_protein_Asp3,_putative_821595..821745_POSITIVE 218 56 22 134 92 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 216 57 15 57 8 NC_009009:SSA_0758|3end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_741909..742059_POSITIVE 216 69 34 45 6 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 214 76 32 92 35 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 212 149 129 57 37 NC_009009:SSA_1910|3end_hypothetical_protein_1902151..1902301_NEGATIVE 212 52 17 109 65 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 209 59 13 148 86 NC_009009:SSA_0549|3end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_545651..545801_POSITIVE