Origin IGS: acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtttgtttgagatctctacctgctggggatcaaaagaggatagatagggagcaaagagagcgcagatgaagaggaccagcaaaatgacacttgaaaaaataaatcgt Mask Tandem Repeat Region ================================================ acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta Find is-nt database================================================ Query_seq: SSA_0500:SSA_0502|SSA_0500:SSA_0502:Peptide ABC transporter, permease protein, putative:Peptide ABC transporter, permease protein, putative:->->:501585..501693 109 acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0500:SSA_0502|SSA_0500:SSA_0502:Peptide ABC transporter, permease protein, putative:Peptide ABC transporter, permease protein, putative:->->:501585..501693 109 acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0500:SSA_0502|SSA_0500:SSA_0502:Peptide ABC transporter, permease protein, putative:Peptide ABC transporter, permease protein, putative:->->:501585..501693 109 acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 8 End: 109 ....... M F S S V I L L V L F I C A L F A P Y L S S F D P Q Q V E I S N K L acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta 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================================================ acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0500:SSA_0502|SSA_0500:SSA_0502:Peptide ABC transporter, permease protein, putative:Peptide ABC transporter, permease protein, putative:->->:501585..501693 109 acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_0500_SSA_0502|Peptide ABC transporter, permease protein, putative:Peptide ABC transporter, permease protein, putative|POSITIVE:POSITIVE|[501585,501693]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta acgatttattttttcaagtgtcattttgctggtcctcttcatctgcgctctctttgctccctatctatcctcttttgatccccagcaggtagagatctcaaacaaacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAUUUAUUUUUUCAAGUGUCAUUUUGCUGGUCCUCUUCAUCUGCGCUCUCUUUGCUCCCUAUCUAUCCUCUUUUGAUCCCCAGCAGGUAGAGAUCUCAAACAAACUA ................(((.....((((..((((.(((..((((((((.......)).............((....))......))))))))))))).))))...))). (-13.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUUGUUUGAGAUCUCUACCUGCUGGGGAUCAAAAGAGGAUAGAUAGGGAGCAAAGAGAGCGCAGAUGAAGAGGACCAGCAAAAUGACACUUGAAAAAAUAAAUCGU ...((..((((...(((((.(((((((....((....))...))).))))......)))))...))))..))..................................... (-16.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 59 13 195 139 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 349 67 23 173 121 NC_009009:SSA_1940|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1927129..1927359_NEGATIVE 348 90 45 138 94 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 342 75 34 144 99 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 335 77 34 103 49 NC_009009:SSA_1902|5end_tRNA_(guanine-N(7)-)-methyltransferase,_putative_1897391..1897621_NEGATIVE 335 70 25 46 1 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 334 95 57 171 131 NC_009009:SSA_2004|5end_Zinc_metalloprotease_zmpB_precursor,_putative_2004930..2005160_NEGATIVE 327 58 11 108 66 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 312 66 24 224 182 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 309 98 51 181 119 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 309 62 30 164 130 NC_009009:SSA_1231|5end_hypothetical_protein_1254758..1254988_NEGATIVE 307 89 41 131 77 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 307 50 1 193 120 NC_009009:SSA_1499|5end_50S_ribosomal_protein_L35,_putative_1504357..1504587_NEGATIVE 301 73 32 105 62 NC_009009:SSA_1128|5end_Voltage_gated_chloride_channel_EriC,_putative_1153250..1153480_POSITIVE 300 68 28 198 164 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 298 90 41 217 153 NC_009009:SSA_1322|5end_Glycosyl_transferase,_putative_1339819..1340049_NEGATIVE 297 79 31 70 8 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 291 89 46 68 25 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 289 60 13 128 83 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 289 58 17 134 84 NC_009009:SSA_1681|5end_ABC-type_bacitracin_resistance_protein_A,_ATPase_component,_putative_1675960..1676190_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 90 43 146 94 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 343 70 25 148 95 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 342 75 34 135 90 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 335 77 34 106 52 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 327 58 11 130 88 NC_009009:SSA_0620|3end_hypothetical_protein_611951..612101_NEGATIVE 323 59 18 71 27 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 316 60 22 51 6 NC_009009:SSA_2184|3end_hypothetical_protein_2183284..2183434_NEGATIVE 309 62 30 116 82 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 307 89 41 127 73 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 300 66 24 75 12 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 296 68 25 60 10 NC_009009:SSA_1224|3end_hypothetical_protein_1247251..1247401_NEGATIVE 295 69 23 129 76 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 295 70 29 136 91 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 291 89 46 71 28 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 289 60 13 135 90 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 287 78 33 119 63 NC_009009:SSA_1238|3end_hypothetical_protein_1262402..1262552_NEGATIVE 286 70 26 150 107 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 286 77 31 125 80 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 286 66 24 106 60 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 283 57 19 108 67 NC_009009:SSA_1803|3end_GTP-binding_protein,_putative_1786599..1786749_NEGATIVE