Origin IGS: agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata .........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 tatttactccgttatagcctctcatctaagtcattaccattataccatgactaggcttacttggctattaagaatgattgtaaataagctaaaaagaaaaaagcagggcaaaactaaccaaagttcagcctcctgcttctgcatgattgcttatccatttaaggcaatgcaagctttaaactagtattttttcaatcctcgct Mask Tandem Repeat Region ================================================ agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata Find is-nt database================================================ Query_seq: SSA_0685:SSA_0686|SSA_0685:SSA_0686:hypothetical protein:Fe2+/Zn2+ uptake regulation protein, putative:->->:669493..669695 203 agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0685:SSA_0686|SSA_0685:SSA_0686:hypothetical protein:Fe2+/Zn2+ uptake regulation protein, putative:->->:669493..669695 203 agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0685:SSA_0686|SSA_0685:SSA_0686:hypothetical protein:Fe2+/Zn2+ uptake regulation protein, putative:->->:669493..669695 203 agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 57 End: 161 ........................................................ M M Q K Q E A E L W L V L P C F F L F S L F T I I L N S Q V S L V M V .......................................... Protein_Len: 60 Strand: - Start: 23 End: 202 ...................... N L A Q M A K F P Y A I M C F C S A S S Q N T K G Q K K R K L K N V I M R L L W T L R T M T Y H Y H S L H S A I V S Y M . agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata 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: 136 End: 165 .......................................................................................................................................ATAGCCAAGTAAGCCTAGTCATGGTATAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 43 HP_score: -3.1 Tail_Score: -2.73203 Start: 74 End: 97 Full_Region: CATGCAGAAGCAGGA GGCTGAACT TTGGTT AGTTTTGCC CTGCTTTTTTCTTTT .........................................................................GGCTGAACTTTGGTTAGTTTTGCC.......................................................................................................... Find igs database================================================ Query_seq: SSA_0685:SSA_0686|SSA_0685:SSA_0686:hypothetical protein:Fe2+/Zn2+ uptake regulation protein, putative:->->:669493..669695 203 agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: NC_009009_SSA_0685_SSA_0686|hypothetical protein:Fe2+/Zn2+ uptake regulation protein, putative|POSITIVE:POSITIVE|[669493,669695]|203 HSP 1 e-value: 5.0E-90 bit: 331.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcnnnnnnnnnnnnagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata agcgaggattgaaaaaatactagtttaaagcttgcattgccttaaatggataagcaatcatgcagaagcaggaggctgaactttggttagttttgccctgcttttttctttttagcttatttacaatcattcttaatagccaagtaagcctagtcatggtataatggtaatgacttagatgagaggctataacggagtaaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGAGGAUUGAAAAAAUACUAGUUUAAAGCUUGCAUUGCCUUAAAUGGAUAAGCAAUCAUGCAGAAGCAGGAGGCUGAACUUUGGUUAGUUUUGCCCUGCUUUUUUCUUUUUAGCUUAUUUACAAUCAUUCUUAAUAGCCAAGUAAGCCUAGUCAUGGUAUAAUGGUAAUGACUUAGAUGAGAGGCUAUAACGGAGUAAAUA .(((((..(((((..........)))))..)))))...........(((((((((((......(((((((((..((.(((((......))))).)))))))))))......)).))))))))).....(((((..((((((.......(..((((((............))))))..)......))))))...)))))..... (-46.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUACUCCGUUAUAGCCUCUCAUCUAAGUCAUUACCAUUAUACCAUGACUAGGCUUACUUGGCUAUUAAGAAUGAUUGUAAAUAAGCUAAAAAGAAAAAAGCAGGGCAAAACUAACCAAAGUUCAGCCUCCUGCUUCUGCAUGAUUGCUUAUCCAUUUAAGGCAAUGCAAGCUUUAAACUAGUAUUUUUUCAAUCCUCGCU (((((((..((((((((((......((.((((((............)))))).)).......))))))....))))...))))))).........((((((((((((((..((((......))))..))..)))))....((.(((((((((.........))))))).)).))............))))))).......... (-41.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 110 64 153 115 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 355 100 54 204 168 NC_009009:SSA_0350|5end_Helicase,_putative_344218..344448_NEGATIVE 317 105 62 99 52 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 309 99 54 227 173 NC_009009:SSA_1440|5end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444721..1444951_NEGATIVE 305 107 70 148 113 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 299 99 52 203 155 NC_009009:SSA_0160|5end_hypothetical_protein_158735..158965_POSITIVE 298 78 31 199 144 NC_009009:SSA_2254|5end_Holliday_junction_DNA_helicase_ruvA,_putative_2250024..2250254_NEGATIVE 295 87 49 171 124 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 295 101 63 177 142 NC_009009:SSA_1664|5end_Phosphatidylethanolamine_N-methyltransferase,_putative_1665189..1665419_NEGATIVE 293 104 61 229 177 NC_009009:SSA_2198|5end_hypothetical_protein_2198585..2198815_NEGATIVE 293 96 60 67 27 NC_009009:SSA_0454|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_457015..457245_NEGATIVE 291 109 62 71 15 NC_009009:SSA_2357|5end_50S_ribosomal_protein_L9,_putative_2358437..2358667_NEGATIVE 289 101 61 222 169 NC_009009:SSA_1164|5end_hypothetical_protein_1191138..1191368_NEGATIVE 281 78 31 113 65 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 277 78 34 69 13 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 276 105 67 193 152 NC_009009:SSA_0415|5end_Permease,_putative_410568..410798_POSITIVE 276 180 137 177 131 NC_009009:SSA_0057|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_60762..60992_POSITIVE 275 107 68 71 30 NC_009009:SSA_1453|5end_hypothetical_protein_1460208..1460438_NEGATIVE 275 103 69 44 1 NC_009009:SSA_0536|5end_B12-dependent_diol_dehydratase_small_subunit,_putative_531342..531572_POSITIVE 274 78 31 173 115 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 110 64 97 48 NC_009009:SSA_0098|3end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_100116..100266_POSITIVE 355 100 54 144 108 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 325 108 64 50 11 NC_009009:SSA_1943|3end_Aspartate_kinase,_putative_1930159..1930309_POSITIVE 317 105 62 109 62 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 309 99 54 109 55 NC_009009:SSA_1441|3end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1444839..1444989_NEGATIVE 306 99 63 98 69 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 305 107 70 148 113 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 300 105 61 102 57 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 296 105 64 151 118 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 295 101 63 144 109 NC_009009:SSA_1665|3end_hypothetical_protein_1665222..1665372_NEGATIVE 293 104 61 135 83 NC_009009:SSA_2199|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2198679..2198829_NEGATIVE 293 96 60 86 46 NC_009009:SSA_0455|3end_Sucrose-6-phosphate_hydrolase,_putative_456996..457146_NEGATIVE 292 110 62 90 47 NC_009009:SSA_0099|3end_hypothetical_protein_100134..100284_NEGATIVE 291 109 62 74 18 NC_009009:SSA_2358|3end_hypothetical_protein_2358434..2358584_NEGATIVE 291 107 61 111 67 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 286 78 31 134 90 NC_009009:SSA_1398|3end_Membrane_protein,_hemolysin_III-like,_putative_1411626..1411776_POSITIVE 277 78 34 72 16 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 277 78 31 149 105 NC_009009:SSA_0549|3end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_545651..545801_POSITIVE 276 105 67 114 73 NC_009009:SSA_0414|3end_hypothetical_protein_410569..410719_POSITIVE 274 76 31 149 95 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE