Origin IGS: aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggctagctaaaatagaattagcatttaagctcatggaaacatgcgagaatcctcgcatgtttttttgattgtgcaaaaacttcccatatccctttggaatccttgctaaatcatgctataattgactt Mask Tandem Repeat Region ================================================ aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc Find is-nt database================================================ Query_seq: SSA_0711:SSA_0712|SSA_0711:SSA_0712:hypothetical protein:P-type ATPase-metal cation transport (calcium efflux), putative:<-<-:696722..696850 129 aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0711:SSA_0712|SSA_0711:SSA_0712:hypothetical protein:P-type ATPase-metal cation transport (calcium efflux), putative:<-<-:696722..696850 129 aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0711:SSA_0712|SSA_0711:SSA_0712:hypothetical protein:P-type ATPase-metal cation transport (calcium efflux), putative:<-<-:696722..696850 129 aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 29 End: 127 ............................ M P K G Y G K F L H N Q K N M R G F S H V S M S L N A N S I L A S .. aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc 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: 87 Start: 7 End: 36 ......TTTGGAATCCTTGCTAAATCATGCTATAAT............................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -12.9 Tail_Score: -3.29461 Start: 61 End: 98 Full_Region: aattagcatttaagc tcatggaaacatgcgag aatc ctcgcatgtttttttga ttgtgcaaaaacttc ............................................................tcatggaaacatgcgagaatcctcgcatgtttttttga............................... TransTerm Strand: - Conf: 100 HP_score: -12.2 Tail_Score: -5.68023 Start: 70 End: 89 Full_Region: ttaagctcatggaaa catgcgag aatc ctcgcatg tttttttgattgtgc .....................................................................catgcgagaatcctcgcatg........................................ Find igs database================================================ Query_seq: SSA_0711:SSA_0712|SSA_0711:SSA_0712:hypothetical protein:P-type ATPase-metal cation transport (calcium efflux), putative:<-<-:696722..696850 129 aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_009009_SSA_0711_SSA_0712|hypothetical protein:P-type ATPase-metal cation transport (calcium efflux), putative|NEGATIVE:NEGATIVE|[696722,696850]|129 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcnnnnnnncatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc aagtcaattatagcatgatttagcaaggattccaaagggatatgggaagtttttgcacaatcaaaaaaacatgcgaggattctcgcatgtttccatgagcttaaatgctaattctattttagctagccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUCAAUUAUAGCAUGAUUUAGCAAGGAUUCCAAAGGGAUAUGGGAAGUUUUUGCACAAUCAAAAAAACAUGCGAGGAUUCUCGCAUGUUUCCAUGAGCUUAAAUGCUAAUUCUAUUUUAGCUAGCCC ..........((((.(((((..((((((((((((........))))..))))))))..)))))...(((((((((((....))))))))))).....(((......)))............)))).... (-34.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGCUAGCUAAAAUAGAAUUAGCAUUUAAGCUCAUGGAAACAUGCGAGAAUCCUCGCAUGUUUUUUUGAUUGUGCAAAAACUUCCCAUAUCCCUUUGGAAUCCUUGCUAAAUCAUGCUAUAAUUGACUU (((((.(((((.......))))).....)))))..(((((((((((((....))))))))))))).(((((..((((....((((...........))))...))))..)))))............... (-33.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 867 100 51 191 142 NC_009009:SSA_0711|5end_hypothetical_protein_696631..696861_NEGATIVE 337 120 73 126 81 NC_009009:SSA_2255|5end_Transcriptional_regulator,_XRE_family,_putative_2250144..2250374_POSITIVE 324 80 35 185 134 NC_009009:SSA_1860|5end_Penicillin-binding_protein_1A,_putative_1854299..1854529_POSITIVE 285 59 13 190 152 NC_009009:SSA_0050|5end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_54612..54842_POSITIVE 277 118 73 191 145 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 274 118 75 71 4 NC_009009:SSA_0166|5end_hypothetical_protein_164641..164871_POSITIVE 267 50 2 78 35 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 264 50 2 134 96 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 254 114 72 40 1 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 251 105 75 73 36 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 249 108 80 32 3 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 244 115 73 71 20 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 240 109 71 53 14 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 236 62 21 201 166 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 236 46 3 50 18 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 232 45 1 47 7 NC_009009:SSA_0955|5end_Aminopeptidase_N,_putative_958519..958749_POSITIVE 230 49 1 184 132 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 229 115 71 117 65 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 228 78 32 199 146 NC_009009:SSA_2085|5end_Glyoxylate_reductase,_NADH-dependent,_putative_2090404..2090634_NEGATIVE 228 56 12 70 14 NC_009009:SSA_1146|5end_Phosphotransferase_system_cellobiose-specific_component_IIA,_putative_1176453..1176683_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 109 65 98 44 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 254 114 72 53 14 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 251 105 75 69 32 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 249 108 80 39 10 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 246 100 51 147 83 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 236 46 3 78 46 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 235 54 16 150 107 NC_009009:SSA_0099|3end_hypothetical_protein_100134..100284_NEGATIVE 229 115 71 106 54 NC_009009:SSA_1469|3end_Shikimate_dehydrogenase,_putative_1475463..1475613_NEGATIVE 228 58 26 38 10 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 225 114 74 114 74 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 224 109 61 56 11 NC_009009:SSA_0939|3end_Inositol_monophosphatase_(Mg++_dependent),_putative_947705..947855_POSITIVE 221 94 60 81 46 NC_009009:SSA_2141|3end_Argininosuccinate_lyase,_putative_2140819..2140969_NEGATIVE 220 113 76 141 98 NC_009009:SSA_0549|3end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_545651..545801_POSITIVE 220 31 2 143 116 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 219 50 3 135 98 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 218 59 14 63 20 NC_009009:SSA_1795|3end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777051..1777201_NEGATIVE 218 119 74 96 35 NC_009009:SSA_0392|3end_hypothetical_protein_388303..388453_POSITIVE 216 111 72 146 106 NC_009009:SSA_2106|3end_Flavin_monoxygenase,_putative_2108015..2108165_NEGATIVE 215 120 72 80 38 NC_009009:SSA_0316|3end_hypothetical_protein_311342..311492_POSITIVE 215 83 43 49 3 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE