Origin IGS: gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcattctcctttcataaggtgcagagtcgagcttaatcaataaagcaagcagactaattcactgctcttaaccttcattgattctgaataacaaataatctccctgcaaaaacaagc Mask Tandem Repeat Region ================================================ gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat Find is-nt database================================================ Query_seq: SSA_0272:SSA_0273|SSA_0272:SSA_0273:Oxidoreductase, aldo/keto reductase family, putative:hypothetical protein:->->:267093..267210 118 gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0272:SSA_0273|SSA_0272:SSA_0273:Oxidoreductase, aldo/keto reductase family, putative:hypothetical protein:->->:267093..267210 118 gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0272:SSA_0273|SSA_0272:SSA_0273:Oxidoreductase, aldo/keto reductase family, putative:hypothetical protein:->->:267093..267210 118 gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat Predict ORF larger than 30AA ================================================ gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat 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================================================ gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0272:SSA_0273|SSA_0272:SSA_0273:Oxidoreductase, aldo/keto reductase family, putative:hypothetical protein:->->:267093..267210 118 gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_009009_SSA_0272_SSA_0273|Oxidoreductase, aldo/keto reductase family, putative:hypothetical protein|POSITIVE:POSITIVE|[267093,267210]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat gcttgtttttgcagggagattatttgttattcagaatcaatgaaggttaagagcagtgaattagtctgcttgctttattgattaagctcgactctgcaccttatgaaaggagaatgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUGUUUUUGCAGGGAGAUUAUUUGUUAUUCAGAAUCAAUGAAGGUUAAGAGCAGUGAAUUAGUCUGCUUGCUUUAUUGAUUAAGCUCGACUCUGCACCUUAUGAAAGGAGAAUGAU .(((.(((((((((((.((.((.....)).))..(((((((((((.....((((((.........)))))).)))))))))))........)))))))......)))).)))...... (-29.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUUCUCCUUUCAUAAGGUGCAGAGUCGAGCUUAAUCAAUAAAGCAAGCAGACUAAUUCACUGCUCUUAACCUUCAUUGAUUCUGAAUAACAAAUAAUCUCCCUGCAAAAACAAGC ........((((....))))..(((((((((((((........)))).(((((.........)))))...........)))))))))............................... (-19.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 98 53 184 136 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 300 104 62 57 13 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 289 110 64 57 3 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 288 100 51 203 139 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 271 100 54 98 57 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 271 101 64 56 19 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 267 74 32 190 143 NC_009009:SSA_0076|5end_ABC_sugar_transporter,_permease_protein,_putative_79847..80077_POSITIVE 266 106 63 217 176 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 264 98 51 220 165 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 262 97 51 136 80 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 260 100 52 47 8 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 259 90 42 73 20 NC_009009:SSA_0461|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_463059..463289_POSITIVE 255 110 64 164 114 NC_009009:SSA_1445|5end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447886..1448116_NEGATIVE 254 96 51 156 106 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 253 84 41 180 134 NC_009009:SSA_1571|5end_Threonyl-tRNA_synthetase,_putative_1575154..1575384_NEGATIVE 252 110 66 114 60 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 252 97 51 82 27 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 251 106 63 111 63 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 250 46 1 217 165 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 249 96 51 83 41 NC_009009:SSA_1628|5end_MutT/nudix_family_protein,_putative_1629864..1630094_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 79 31 80 27 NC_009009:SSA_0669|3end_ATP_dependent_protease,_putative_651450..651600_NEGATIVE 301 88 50 66 29 NC_009009:SSA_0143|3end_Conserved_uncharacterized_protein_137880..138030_POSITIVE 300 104 62 56 12 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 290 100 52 139 85 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE 284 97 53 143 85 NC_009009:SSA_0714|3end_hypothetical_protein_700649..700799_POSITIVE 281 104 62 128 75 NC_009009:SSA_0584|3end_hypothetical_protein_576689..576839_POSITIVE 267 104 63 149 112 NC_009009:SSA_2351|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_ATPase_component,_putative_2352785..2352935_NEGATIVE 259 90 42 80 27 NC_009009:SSA_0460|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_463146..463296_POSITIVE 257 98 51 116 65 NC_009009:SSA_0900|3end_Tetratricopeptide_repeat_(TPR)_family_protein_892377..892527_POSITIVE 255 70 32 113 69 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 250 98 51 119 57 NC_009009:SSA_0668|3end_hypothetical_protein_651431..651581_POSITIVE 250 46 1 122 70 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 245 97 51 136 77 NC_009009:SSA_1179|3end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1206640..1206790_NEGATIVE 245 101 65 37 1 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 245 101 66 83 43 NC_009009:SSA_0053|3end_Beta-galactosidase,_putative_58615..58765_POSITIVE 244 38 1 111 66 NC_009009:SSA_1761|3end_Hemolysin_(containing_CBS_domains),_putative_1747437..1747587_NEGATIVE 243 110 61 144 85 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 242 98 51 58 12 NC_009009:SSA_1975|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1970257..1970407_NEGATIVE 241 35 1 136 101 NC_009009:SSA_1905|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1899276..1899426_NEGATIVE 241 94 51 149 96 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE