Origin IGS: gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctgctcttttttattacattttaatgacagagtgacaatcagtttgacagcggcgtttttataatgatatgataaaatcagctcaatattgaaggagataagac Mask Tandem Repeat Region ================================================ gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc Find is-nt database================================================ Query_seq: SSA_2242:SSA_2243|SSA_2242:SSA_2243:hypothetical protein:Conserved uncharacterized protein:<-<-:2238754..2238858 105 gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2242:SSA_2243|SSA_2242:SSA_2243:hypothetical protein:Conserved uncharacterized protein:<-<-:2238754..2238858 105 gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2242:SSA_2243|SSA_2242:SSA_2243:hypothetical protein:Conserved uncharacterized protein:<-<-:2238754..2238858 105 gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 6 End: 104 ..... M S F N I E L I L S Y H Y K N A A V K L I V T L S L K C N K K E Q . gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc 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================================================ gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2242:SSA_2243|SSA_2242:SSA_2243:hypothetical protein:Conserved uncharacterized protein:<-<-:2238754..2238858 105 gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_009009_SSA_2242_SSA_2243|hypothetical protein:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2238754,2238858]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc gtcttatctccttcaatattgagctgattttatcatatcattataaaaacgccgctgtcaaactgattgtcactctgtcattaaaatgtaataaaaaagagcagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUUAUCUCCUUCAAUAUUGAGCUGAUUUUAUCAUAUCAUUAUAAAAACGCCGCUGUCAAACUGAUUGUCACUCUGUCAUUAAAAUGUAAUAAAAAAGAGCAGC ......................((((.((((.......((((.(((..(((..(.((.(((.....))).)))..)))..))).))))........)))).)))) ( -9.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUGCUCUUUUUUAUUACAUUUUAAUGACAGAGUGACAAUCAGUUUGACAGCGGCGUUUUUAUAAUGAUAUGAUAAAAUCAGCUCAAUAUUGAAGGAGAUAAGAC ((((((.....((((((.....))))))((((.((.....)).))))..)))))).((((.(((.(((..((((...))))..))).))).)))).......... (-17.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 80 31 171 122 NC_009009:SSA_2242|5end_hypothetical_protein_2238663..2238893_NEGATIVE 285 79 51 202 175 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 273 97 51 83 39 NC_009009:SSA_1275|5end_hypothetical_protein_1297606..1297836_NEGATIVE 272 85 50 190 149 NC_009009:SSA_2007|5end_Chaperone_protein_dnaK/HSP70,_putative_2009272..2009502_NEGATIVE 266 91 51 230 191 NC_009009:SSA_1274|5end_hypothetical_protein_1297454..1297684_NEGATIVE 255 88 50 200 152 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 254 78 50 231 201 NC_009009:SSA_1074|5end_Pyrroline-5-carboxylate_reductase,_putative_1092151..1092381_POSITIVE 253 87 50 70 29 NC_009009:SSA_1602|5end_Exoribonuclease,_VacB/Rnb_family,_putative_1609370..1609600_NEGATIVE 247 38 7 129 99 NC_009009:SSA_0249|5end_hypothetical_protein_241751..241981_POSITIVE 244 41 1 136 92 NC_009009:SSA_0070|5end_Acetylxylan_esterase,_putative_73833..74063_POSITIVE 240 70 22 51 1 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 239 89 48 87 39 NC_009009:SSA_0961|5end_Possible_ketopantoate_reductase_PanE/ApbA,_putative_969913..970143_POSITIVE 234 77 49 210 182 NC_009009:SSA_0533|5end_Glycerol_dehydratase_large_subunit_pduC,_putative_528970..529200_POSITIVE 233 79 52 44 16 NC_009009:SSA_0442|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_442237..442467_POSITIVE 225 31 1 209 180 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 223 61 24 220 181 NC_009009:SSA_1998|5end_Trigger_factor,_putative_1996331..1996561_NEGATIVE 222 59 17 195 142 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 219 80 51 54 24 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 218 57 12 57 15 NC_009009:SSA_2330|5end_Acetyltransferase,_putative_2333655..2333885_NEGATIVE 217 90 44 152 100 NC_009009:SSA_2220|5end_Galactosyltransferase,_putative_2221439..2221669_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 59 12 150 115 NC_009009:SSA_2327|3end_hypothetical_protein_2331400..2331550_POSITIVE 255 88 50 90 42 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 247 83 55 124 99 NC_009009:SSA_0793|3end_DNA-entry_nuclease,_putative_775799..775949_POSITIVE 247 38 7 142 112 NC_009009:SSA_0248|3end_hypothetical_protein_241844..241994_POSITIVE 239 89 48 71 23 NC_009009:SSA_0960|3end_Sensor_protein_ciaH,_putative_969977..970127_POSITIVE 228 39 3 42 9 NC_009009:SSA_2030|3end_hypothetical_protein_2036514..2036664_NEGATIVE 227 80 33 66 12 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 225 70 22 84 39 NC_009009:SSA_1041|3end_Sugar_ABC_transporter,_permease_protein,_putative_1057434..1057584_POSITIVE 224 80 50 149 114 NC_009009:SSA_0999|3end_Biotin--[acetyl-CoA-carboxylase]_ligase,_putative_998781..998931_NEGATIVE 223 61 24 140 101 NC_009009:SSA_1999|3end_hypothetical_protein_1996411..1996561_NEGATIVE 223 88 46 68 42 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 217 90 44 136 84 NC_009009:SSA_2221|3end_Cps9E,_putative_2221455..2221605_NEGATIVE 216 65 32 57 23 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 215 82 50 99 68 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 208 65 21 150 96 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 205 75 52 59 29 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 204 81 50 144 115 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 204 81 47 138 98 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE 204 45 1 95 48 NC_009009:SSA_0516|3end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_515140..515290_POSITIVE 203 39 1 132 88 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE