Origin IGS: aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagctaggataggtcctcttcgctggaaagtcctattggcactttctagtaattcggcaccttactatcatttcagaaaaataaatacataagagctctttcagggctcttttttgaaaccagttgtaaaatttgttatactatcactagaaaaggagtgatttt Mask Tandem Repeat Region ================================================ aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta Find is-nt database================================================ Query_seq: SSA_1305:SSA_1306|SSA_1305:SSA_1306:hypothetical protein:Trk transporter NAD+ binding protein-K+ transport, putative:<-<-:1324170..1324334 165 aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1305:SSA_1306|SSA_1305:SSA_1306:hypothetical protein:Trk transporter NAD+ binding protein-K+ transport, putative:<-<-:1324170..1324334 165 aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1305:SSA_1306|SSA_1305:SSA_1306:hypothetical protein:Trk transporter NAD+ binding protein-K+ transport, putative:<-<-:1324170..1324334 165 aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta Predict ORF larger than 30AA ================================================ aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta 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: 86 Start: 24 End: 53 .......................TTTGAAACCAGTTGTAAAATTTGTTATACT................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -8.7 Tail_Score: -5.00884 Start: 57 End: 73 Full_Region: aaaataaatacataa gagctct ttc agggctc ttttttgaaaccagt ........................................................gagctctttcagggctc............................................................................................ Find igs database================================================ Query_seq: SSA_1305:SSA_1306|SSA_1305:SSA_1306:hypothetical protein:Trk transporter NAD+ binding protein-K+ transport, putative:<-<-:1324170..1324334 165 aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: NC_009009_SSA_1305_SSA_1306|hypothetical protein:Trk transporter NAD+ binding protein-K+ transport, putative|NEGATIVE:NEGATIVE|[1324170,1324334]|165 HSP 1 e-value: 7.0E-89 bit: 327.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta aaaatcactccttttctagtgatagtataacaaattttacaactggtttcaaaaaagagccctgaaagagctcttatgtatttatttttctgaaatgatagtaaggtgccgaattactagaaagtgccaataggactttccagcgaagaggacctatcctagcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCACUCCUUUUCUAGUGAUAGUAUAACAAAUUUUACAACUGGUUUCAAAAAAGAGCCCUGAAAGAGCUCUUAUGUAUUUAUUUUUCUGAAAUGAUAGUAAGGUGCCGAAUUACUAGAAAGUGCCAAUAGGACUUUCCAGCGAAGAGGACCUAUCCUAGCUA ........((((((((.((((((.(((..........)))....(((.((....((((((.(.....).))))))......(((((((...)))))))......)).)))..)))))).((((((.((....))))))))....))))))))............. (-33.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCUAGGAUAGGUCCUCUUCGCUGGAAAGUCCUAUUGGCACUUUCUAGUAAUUCGGCACCUUACUAUCAUUUCAGAAAAAUAAAUACAUAAGAGCUCUUUCAGGGCUCUUUUUUGAAACCAGUUGUAAAAUUUGUUAUACUAUCACUAGAAAAGGAGUGAUUUU (((((.((..((((((...(..(((((((((((....)).)))))))))..)...)).))))........(((((((((............(((((((.....)))))))))))))))))))))))................((((((........))))))... (-43.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 853 140 91 231 182 NC_009009:SSA_1305|5end_hypothetical_protein_1324079..1324309_NEGATIVE 322 129 85 203 152 NC_009009:SSA_1256|5end_NAD-dependent_deacetylase,_putative_1283094..1283324_NEGATIVE 315 147 101 71 19 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 286 155 126 105 77 NC_009009:SSA_1362|5end_ORFB,_transposon_ISSsa2_1377911..1378141_POSITIVE 286 155 126 105 77 NC_009009:SSA_0266|5end_ORFB,_transposon_ISSsa1_260134..260364_POSITIVE 284 140 98 89 45 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 284 159 118 139 91 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 271 158 119 44 6 NC_009009:SSA_0396|5end_hypothetical_protein_393595..393825_NEGATIVE 269 90 42 89 41 NC_009009:SSA_0318|5end_Secreted_metalloendopeptidase_Gcp_311701..311931_POSITIVE 263 144 103 154 119 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 263 95 56 174 133 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 263 150 104 230 195 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 262 159 118 214 174 NC_009009:SSA_1657|5end_hypothetical_protein_1653231..1653461_NEGATIVE 262 146 103 147 94 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 261 155 119 73 39 NC_009009:SSA_0427|5end_DNA-binding_transcriptional_activator,_SARP_family,_putative_424497..424727_POSITIVE 261 150 101 216 156 NC_009009:SSA_0424|5end_Exopolysaccharide_biosynthesis_protein,_putative_422233..422463_NEGATIVE 258 155 118 172 131 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 257 129 90 87 49 NC_009009:SSA_1164|5end_hypothetical_protein_1191138..1191368_NEGATIVE 257 159 113 63 6 NC_009009:SSA_0203|5end_hypothetical_protein_201322..201552_POSITIVE 256 75 39 67 31 NC_009009:SSA_1375|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1394827..1395057_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 75 37 87 44 NC_009009:SSA_2235|3end_Conserved_uncharacterized_protein_2234971..2235121_NEGATIVE 284 159 118 130 82 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 269 90 42 99 51 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE 268 139 92 60 18 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 260 159 136 132 109 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 257 159 113 63 6 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 256 95 52 113 58 NC_009009:SSA_1032|3end_30S_ribosomal_protein_subunit_S20,_putative_1048313..1048463_NEGATIVE 253 110 61 108 45 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 253 158 118 91 43 NC_009009:SSA_0705|3end_hypothetical_protein_690552..690702_NEGATIVE 247 99 53 61 17 NC_009009:SSA_2189|3end_hypothetical_protein_2190279..2190429_NEGATIVE 242 110 61 126 73 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 238 72 52 58 37 NC_009009:SSA_1701|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1691299..1691449_NEGATIVE 235 150 119 69 35 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 234 144 103 91 41 NC_009009:SSA_2154|3end_Conserved_uncharacterized_protein_2154762..2154912_NEGATIVE 233 150 105 47 1 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 230 156 114 93 56 NC_009009:SSA_1913|3end_Xanthine/uracil_permease_family_protein,_putative_1903245..1903395_NEGATIVE 230 159 117 60 7 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 230 139 96 59 7 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 230 110 61 137 80 NC_009009:SSA_0549|3end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_545651..545801_POSITIVE 228 160 117 44 1 NC_009009:SSA_2096|3end_ATP-dependent_protease,_ATP-binding_subunit,_putative_2099557..2099707_NEGATIVE