Origin IGS: gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact .........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 agtctcgaaagaatctggaaaaaattccagattcttttttctgtgttgggccagtctaggcaagtatttttctgaagtaagagaaactaatacagaattttaagaaagcctttgcaaaatttgattcttttctttataataaaaattaaataggataatatacatttatacagaaaaggagaagttc Mask Tandem Repeat Region ================================================ gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact Find is-nt database================================================ Query_seq: SSA_1750:SSA_1751|SSA_1750:SSA_1751:Extracellular nuclease, putative:Dextran glucosidase, alpha amylase family, putative:<-<-:1738013..1738199 187 gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1750:SSA_1751|SSA_1750:SSA_1751:Extracellular nuclease, putative:Dextran glucosidase, alpha amylase family, putative:<-<-:1738013..1738199 187 gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1750:SSA_1751|SSA_1750:SSA_1751:Extracellular nuclease, putative:Dextran glucosidase, alpha amylase family, putative:<-<-:1738013..1738199 187 gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact Predict ORF larger than 30AA ================================================ gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact 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: 91 Start: 48 End: 77 ...............................................TTTGCAAAATTTGATTCTTTTCTTTATAAT.............................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1750:SSA_1751|SSA_1750:SSA_1751:Extracellular nuclease, putative:Dextran glucosidase, alpha amylase family, putative:<-<-:1738013..1738199 187 gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: NC_009009_SSA_1750_SSA_1751|Extracellular nuclease, putative:Dextran glucosidase, alpha amylase family, putative|NEGATIVE:NEGATIVE|[1738013,1738199]|187 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact gaacttctccttttctgtataaatgtatattatcctatttaatttttattataaagaaaagaatcaaattttgcaaaggctttcttaaaattctgtattagtttctcttacttcagaaaaatacttgcctagactggcccaacacagaaaaaagaatctggaattttttccagattctttcgagact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACUUCUCCUUUUCUGUAUAAAUGUAUAUUAUCCUAUUUAAUUUUUAUUAUAAAGAAAAGAAUCAAAUUUUGCAAAGGCUUUCUUAAAAUUCUGUAUUAGUUUCUCUUACUUCAGAAAAAUACUUGCCUAGACUGGCCCAACACAGAAAAAAGAAUCUGGAAUUUUUUCCAGAUUCUUUCGAGACU .....(((((((((((.(((((.((...((((.......))))...))))))).))))))).......(((((....((((.(((.........(((((..(((((........))))))))))......)))..)))).....))))).(((((((((((((....))))))))))))).)))).. (-38.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUCGAAAGAAUCUGGAAAAAAUUCCAGAUUCUUUUUUCUGUGUUGGGCCAGUCUAGGCAAGUAUUUUUCUGAAGUAAGAGAAACUAAUACAGAAUUUUAAGAAAGCCUUUGCAAAAUUUGAUUCUUUUCUUUAUAAUAAAAAUUAAAUAGGAUAAUAUACAUUUAUACAGAAAAGGAGAAGUUC ..(((.((((((((((((((....))))))))))))))((((((((((((((......))).....(((((((......)))))))))))))))))).....)))..((....))..(((((..(((((((((.(((((.....((((.......))))......))))).))))))))).))))). (-48.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 852 140 91 231 182 NC_009009:SSA_1750|5end_Extracellular_nuclease,_putative_1737922..1738152_NEGATIVE 299 148 102 80 27 NC_009009:SSA_0443|5end_Possible_ABC-type_efflux_pump_permease_component,_putative_442877..443107_POSITIVE 294 158 113 89 28 NC_009009:SSA_2153|5end_ABC-type_transporter_(uncharacterized),_permease_component,_putative_2154664..2154894_NEGATIVE 286 140 91 56 2 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 274 179 134 210 160 NC_009009:SSA_1464|5end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1471516..1471746_NEGATIVE 274 141 111 48 21 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 273 138 91 225 180 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 272 139 91 151 101 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 266 147 104 212 170 NC_009009:SSA_0779|5end_Glycogen_phosphorylase,_putative_762209..762439_POSITIVE 258 120 78 226 189 NC_009009:SSA_1603|5end_hypothetical_protein_1610034..1610264_NEGATIVE 258 158 115 140 92 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 253 177 136 227 189 NC_009009:SSA_1128|5end_Voltage_gated_chloride_channel_EriC,_putative_1153250..1153480_POSITIVE 250 149 105 197 151 NC_009009:SSA_1256|5end_NAD-dependent_deacetylase,_putative_1283094..1283324_NEGATIVE 248 170 125 203 153 NC_009009:SSA_2315|5end_Conserved_uncharacterized_protein_2316945..2317175_NEGATIVE 248 180 131 199 152 NC_009009:SSA_1365|5end_FmtA-like_protein,_putative_1382299..1382529_NEGATIVE 246 136 106 175 146 NC_009009:SSA_1686|5end_hypothetical_protein_1679176..1679406_POSITIVE 238 118 78 60 20 NC_009009:SSA_0523|5end_Aldehyde_dehydrogenase,_putative_521637..521867_POSITIVE 235 140 94 140 87 NC_009009:SSA_0955|5end_Aminopeptidase_N,_putative_958519..958749_POSITIVE 234 105 64 126 75 NC_009009:SSA_1676|5end_Transcriptional_regulator,_LytTr_family,_putative_1671313..1671543_NEGATIVE 234 161 126 191 153 NC_009009:SSA_0351|5end_Signal_peptidase_I,_putative_344907..345137_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 177 134 77 36 NC_009009:SSA_1301|3end_Conserved_uncharacterized_protein,_possible_surface_protein_1319010..1319160_NEGATIVE 291 180 145 49 10 NC_009009:SSA_1964|3end_conserved_uncharacterized_protein_1960996..1961146_NEGATIVE 291 180 144 66 31 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 287 140 95 140 86 NC_009009:SSA_0442|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_443030..443180_POSITIVE 274 179 134 78 28 NC_009009:SSA_1465|3end_Conserved_uncharacterized_protein_1471648..1471798_NEGATIVE 274 141 111 48 21 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 273 138 91 146 101 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 266 140 94 87 36 NC_009009:SSA_1604|3end_Protein-export_membrane_protein_secG,_putative_1610198..1610348_NEGATIVE 253 177 136 84 46 NC_009009:SSA_1127|3end_H2O-forming_NADH_dehydrogenase,_putative_1153187..1153337_POSITIVE 252 149 104 55 13 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 238 118 78 53 13 NC_009009:SSA_0522|3end_Ethanolamine_utilization_protein,_putative_521710..521860_POSITIVE 234 105 64 103 52 NC_009009:SSA_1678|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1671336..1671486_NEGATIVE 232 180 131 74 18 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 232 176 134 80 29 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 232 180 135 55 4 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 231 140 91 103 56 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 230 169 126 79 39 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 228 140 101 150 102 NC_009009:SSA_1112|3end_Cell_wall_surface_anchor_family_protein,_putative_1139738..1139888_POSITIVE 228 139 91 144 97 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 226 139 101 121 80 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE