Origin IGS: gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcagatttatttaatttataaggatttttctatggtctattttttcttttgttttcaaaaatagactataaaatgctttgtgtcaatttttttaaaaaatttttatataattatagttatatatatagctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataatctcctaaataatcatctagttacaatagttttattatacaacattccattttagttagctatatatataactataattatataaaaattttttaaaaaaattgacacaaagcattttatagtctatttttgaaaacaaaagaaaaaatagaccatagaaaaatccttataaattaaataaatctgagagtatctcagattctactttaatgtttaacattttagaaatgctatcatgaagtttttaagatctatttctttgaatataaagaaaaaagattcactaatgaatctttcctcttttaattcaggtgttagaacctaagttctcacctc Mask Tandem Repeat Region ================================================ gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcagatttatttaatttataaggatttttctatggtctattttttcttttgttttcaaaaatagactataaaatgctttgtgtcaatttttttaaaaaatttttatataattatagttatatatatagctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt Find is-nt database================================================ Query_seq: SSA_0905:SSA_0906|SSA_0905:SSA_0906:CshA-like fibrillar surface protein B:CshA-like fibrillar surface protein C:->->:909121..909461 341 gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcagatttatttaatttataaggatttttctatggtctattttttcttttgttttcaaaaatagactataaaatgctttgtgtcaatttttttaaaaaatttttatataattatagttatatatatagctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0905:SSA_0906|SSA_0905:SSA_0906:CshA-like fibrillar surface protein B:CshA-like fibrillar surface protein C:->->:909121..909461 341 gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcagatttatttaatttataaggatttttctatggtctattttttcttttgttttcaaaaatagactataaaatgctttgtgtcaatttttttaaaaaatttttatataattatagttatatatatagctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0905:SSA_0906|SSA_0905:SSA_0906:CshA-like fibrillar surface protein B:CshA-like fibrillar surface protein C:->->:909121..909461 341 gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcagatttatttaatttataaggatttttctatggtctattttttcttttgttttcaaaaatagactataaaatgctttgtgtcaatttttttaaaaaatttttatataattatagttatatatatagctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcagatttatttaatttataaggatttttctatggtctattttttcttttgttttcaaaaatagactataaaatgctttgtgtcaatttttttaaaaaatttttatataattatagttatatatatagctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 15 End: 104 .............. T R V G S N F S S L N M L S D K K K I N L S I S R L F K M M ............................................................................................................................................................................................................................................. gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcagatttatttaatttataaggatttttctatggtctattttttcttttgttttcaaaaatagactataaaatgctttgtgtcaatttttttaaaaaatttttatataattatagttatatatatagctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt 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: 85 Start: 207 End: 236 ..............................................................................................................................................................................................................ATTGACACAAAGCATTTTATAGTCTATTTT......................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 274 End: 303 .................................................................................................................................................................................................................................................................................ATAGCTAACTAAAATGGAATGTTGTATAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcagatttatttaatttataaggatttttctatggtctattttttcttttgttttcaaaaatagactataaaatgctttgtgtcaatttttttaaaaaatttttatataattatagttatatatatagctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -9.5 Tail_Score: -4.1891 Start: 37 End: 66 Full_Region: ACACCTGAATTAAAA GAGGAAAGATTCA TTAG TGAATCTTTTTTC TTTATATTCAAAGAA ....................................GAGGAAAGATTCATTAGTGAATCTTTTTTC................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 88 HP_score: -9.5 Tail_Score: -4.65182 Start: 138 End: 154 Full_Region: AACATTAAAGTAGAA TCTGAGA TAC TCTCAGA TTTATTTAATTTATA .........................................................................................................................................TCTGAGATACTCTCAGA........................................................................................................................................................................................... TransTerm Strand: - Conf: 82 HP_score: -9.5 Tail_Score: -3.64523 Start: 138 End: 154 Full_Region: tataaattaaataaa tctgaga gta tctcaga ttctactttaatgtt .........................................................................................................................................tctgagagtatctcaga........................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0905:SSA_0906|SSA_0905:SSA_0906:CshA-like fibrillar surface protein B:CshA-like fibrillar surface protein C:->->:909121..909461 341 gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcagatttatttaatttataaggatttttctatggtctattttttcttttgttttcaaaaatagactataaaatgctttgtgtcaatttttttaaaaaatttttatataattatagttatatatatagctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt Intra-Species Hit: Count: 1 Min: 1 Max: 341 Len: 341 Subject: NC_009009_SSA_0905_SSA_0906|CshA-like fibrillar surface protein B:CshA-like fibrillar surface protein C|POSITIVE:POSITIVE|[909121,909461]|341 HSP 1 e-value: 2.0E-81 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcag............................................................................................................................................................................................ gaggtgagaacttaggttctaacacctgaattaaaagaggaaagattcattagtgaatcttttttctttatattcaaagaaatagatcttaaaaacttcatgatagcatttctaaaatgttaaacattaaagtagaatctgagatactctcag............................................................................................................................................................................................ HSP 2 e-value: 7.0E-29 bit: 129.0 Len: 65 Query Start:277 Query End:341 Subject Strand: POSITIVE Subject Start: 277 Subject End: 341 ....................................................................................................................................................................................................................................................................................gctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt ....................................................................................................................................................................................................................................................................................gctaactaaaatggaatgttgtataataaaactattgtaactagatgattatttaggagattatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGUGAGAACUUAGGUUCUAACACCUGAAUUAAAAGAGGAAAGAUUCAUUAGUGAAUCUUUUUUCUUUAUAUUCAAAGAAAUAGAUCUUAAAAACUUCAUGAUAGCAUUUCUAAAAUGUUAAACAUUAAAGUAGAAUCUGAGAUACUCUCAGAUUUAUUUAAUUUAUAAGGAUUUUUCUAUGGUCUAUUUUUUCUUUUGUUUUCAAAAAUAGACUAUAAAAUGCUUUGUGUCAAUUUUUUUAAAAAAUUUUUAUAUAAUUAUAGUUAUAUAUAUAGCUAACUAAAAUGGAAUGUUGUAUAAUAAAACUAUUGUAACUAGAUGAUUAUUUAGGAGAUUAUU .((((((((((....)))))..)))))((((..((((((((((((((((....))))))))))))))))..)))).....(((((.(((((((....((((..(((((((((......((((...((((((...(((((((((.....))))))))).)))))).(((((((...(((.((((((((((((((............)))))))))))))))))..))))))).....................((((((((....))))))))......))))......)))))))))(((((((....))))))).....))))...)))))))..))))) (-82.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUCUCCUAAAUAAUCAUCUAGUUACAAUAGUUUUAUUAUACAACAUUCCAUUUUAGUUAGCUAUAUAUAUAACUAUAAUUAUAUAAAAAUUUUUUAAAAAAAUUGACACAAAGCAUUUUAUAGUCUAUUUUUGAAAACAAAAGAAAAAAUAGACCAUAGAAAAAUCCUUAUAAAUUAAAUAAAUCUGAGAGUAUCUCAGAUUCUACUUUAAUGUUUAACAUUUUAGAAAUGCUAUCAUGAAGUUUUUAAGAUCUAUUUCUUUGAAUAUAAAGAAAAAAGAUUCACUAAUGAAUCUUUCCUCUUUUAAUUCAGGUGUUAGAACCUAAGUUCUCACCUC ((((((((....(((((....(((.......)))..)))))............((((((..((((....(((((((......))))))).....(((((((((.....((((.((((..((((((.((((((((((............)))))))))).))))))....................((((((((.....))))))))...))))..)))).....))))))))).))))...)))))).....)))).))))....(((((..(((((..(((((((((....)))))))))..)))))..)))))((((..(((((....))))))))).. (-62.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 64 27 144 102 NC_009009:SSA_1349|5end_Transcriptional_regulator,_biotin_repressor_family,_putative_1365918..1366148_POSITIVE 232 78 39 96 51 NC_009009:SSA_0306|5end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_302590..302820_POSITIVE 224 40 1 161 121 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 222 204 170 73 38 NC_009009:SSA_1184|5end_DNA_topoisomerase_I,_putative_1213605..1213835_NEGATIVE 220 157 129 185 153 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 215 338 293 190 156 NC_009009:SSA_1537|5end_Conserved_uncharacterized_protein_1544441..1544671_NEGATIVE 215 60 16 88 31 NC_009009:SSA_0136|5end_ABC_transporter,_Zn_porter,_putative_131014..131244_POSITIVE 213 54 15 44 3 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 210 201 165 108 67 NC_009009:SSA_2085|5end_Glyoxylate_reductase,_NADH-dependent,_putative_2090404..2090634_NEGATIVE 210 160 117 229 181 NC_009009:SSA_1646|5end_hypothetical_protein_1646771..1647001_NEGATIVE 210 50 1 68 26 NC_009009:SSA_0206|5end_hypothetical_protein_204256..204486_POSITIVE 208 39 2 209 166 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 205 69 23 104 58 NC_009009:SSA_1801|5end_hypothetical_protein_1783314..1783544_NEGATIVE 205 216 172 122 82 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 204 66 25 205 163 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 203 206 175 90 60 NC_009009:SSA_2282|5end_Phage_infection_protein,_putative_2285337..2285567_NEGATIVE 203 206 162 131 85 NC_009009:SSA_1786|5end_Conserved_uncharacterized_protein_1770244..1770474_NEGATIVE 201 207 171 116 81 NC_009009:SSA_0915|5end_hypothetical_protein_927542..927772_POSITIVE 199 59 12 181 140 NC_009009:SSA_2268|5end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_2267228..2267458_POSITIVE 199 200 151 111 56 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 426 69 27 57 15 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 283 208 174 129 86 NC_009009:SSA_1149|3end_Glycosyl_hydrolase,_family_1,_putative_1179876..1180026_POSITIVE 260 65 38 60 33 NC_009009:SSA_0904|3end_CshA-like_fibrillar_surface_protein_A_902958..903108_POSITIVE 244 178 131 113 53 NC_009009:SSA_0688|3end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_672132..672282_POSITIVE 233 64 27 105 63 NC_009009:SSA_1348|3end_hypothetical_protein_1365959..1366109_POSITIVE 224 40 1 69 29 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 222 49 5 49 1 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 220 157 129 54 22 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 215 60 16 91 34 NC_009009:SSA_0135|3end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_131097..131247_POSITIVE 214 176 134 65 25 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 212 48 1 61 3 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 211 71 35 94 55 NC_009009:SSA_0822|3end_Large_conductance_mechano-sensitive_ion_channel,_putative_801589..801739_NEGATIVE 210 201 165 115 74 NC_009009:SSA_2086|3end_hypothetical_protein_2090397..2090547_NEGATIVE 210 50 1 71 29 NC_009009:SSA_2393|3end_Transcriptional_regulator,_XRE_family,_putative_204339..204489_POSITIVE 209 234 191 143 99 NC_009009:SSA_2271|3end_hypothetical_protein_2272238..2272388_NEGATIVE 205 69 23 49 3 NC_009009:SSA_1802|3end_Snf2_family_protein,_putative_1783369..1783519_NEGATIVE 203 206 162 74 28 NC_009009:SSA_1787|3end_Diaminopimelate_decarboxylase,_putative_1770301..1770451_NEGATIVE 200 154 118 61 28 NC_009009:SSA_1927|3end_Exfoliative_toxin,_putative_1914956..1915106_NEGATIVE 199 59 12 63 22 NC_009009:SSA_2267|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2267190..2267340_POSITIVE 199 200 151 118 63 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE