Origin IGS: attatactattaagtatattttccgatggtgattcgaccaagcagattttttctgctttttttgttataataaactcattgaatgtttatgatgtgaaaggaaagacaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgtctttcctttcacatcataaacattcaatgagtttattataacaaaaaaagcagaaaaaatctgcttggtcgaatcaccatcggaaaatatacttaatagtataat Mask Tandem Repeat Region ================================================ attatactattaagtatattttccgatggtgattcgaccaagcagattttttctgctttttttgttataataaactcattgaatgtttatgatgtgaaaggaaagacaa Find is-nt database================================================ Query_seq: SSA_0857:SSA_0858|SSA_0857:SSA_0858:hypothetical protein:DTDP-L-rhamnose synthase, putative:->->:845543..845651 109 attatactattaagtatattttccgatggtgattcgaccaagcagattttttctgctttttttgttataataaactcattgaatgtttatgatgtgaaaggaaagacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0857:SSA_0858|SSA_0857:SSA_0858:hypothetical protein:DTDP-L-rhamnose synthase, putative:->->:845543..845651 109 attatactattaagtatattttccgatggtgattcgaccaagcagattttttctgctttttttgttataataaactcattgaatgtttatgatgtgaaaggaaagacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0857:SSA_0858|SSA_0857:SSA_0858:hypothetical protein:DTDP-L-rhamnose synthase, putative:->->:845543..845651 109 attatactattaagtatattttccgatggtgattcgaccaagcagattttttctgctttttttgttataataaactcattgaatgtttatgatgtgaaaggaaagacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attatactattaagtatattttccgatggtgattcgaccaagcagattttttctgctttttttgttataataaactcattgaatgtttatgatgtgaaaggaaagacaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 1 End: 108 M I L L S I F S D G D S T K Q I F S A F F V I I N S L N V Y D V K G K T . attatactattaagtatattttccgatggtgattcgaccaagcagattttttctgctttttttgttataataaactcattgaatgtttatgatgtgaaaggaaagacaa 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================================================ attatactattaagtatattttccgatggtgattcgaccaagcagattttttctgctttttttgttataataaactcattgaatgtttatgatgtgaaaggaaagacaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 58 HP_score: -5.7 Tail_Score: -3.16564 Start: 42 End: 56 Full_Region: attataacaaaaaaa gcaga aaaaa tctgc ttggtcgaatcacca .........................................gcagaaaaaatctgc..................................................... Find igs database================================================ Query_seq: SSA_0857:SSA_0858|SSA_0857:SSA_0858:hypothetical protein:DTDP-L-rhamnose synthase, putative:->->:845543..845651 109 attatactattaagtatattttccgatggtgattcgaccaagcagattttttctgctttttttgttataataaactcattgaatgtttatgatgtgaaaggaaagacaa Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_0857_SSA_0858|hypothetical protein:DTDP-L-rhamnose synthase, putative|POSITIVE:POSITIVE|[845543,845651]|109 HSP 1 e-value: 4.0E-18 bit: 91.7 Len: 46 Query Start:1 Query End:46 Subject Strand: POSITIVE Subject Start: 1 Subject End: 46 attatactattaagtatattttccgatggtgattcgaccaagcaga............................................................... attatactattaagtatattttccgatggtgattcgaccaagcaga............................................................... HSP 2 e-value: 4.0E-18 bit: 91.7 Len: 46 Query Start:64 Query End:109 Subject Strand: POSITIVE Subject Start: 64 Subject End: 109 ...............................................................gttataataaactcattgaatgtttatgatgtgaaaggaaagacaa ...............................................................gttataataaactcattgaatgtttatgatgtgaaaggaaagacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUACUAUUAAGUAUAUUUUCCGAUGGUGAUUCGACCAAGCAGAUUUUUUCUGCUUUUUUUGUUAUAAUAAACUCAUUGAAUGUUUAUGAUGUGAAAGGAAAGACAA ..((((((....)))))).(((((..((((......)))).(((((.....)))))...(((..(....((((((.........))))))...)..))))))))..... (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCUUUCCUUUCACAUCAUAAACAUUCAAUGAGUUUAUUAUAACAAAAAAAGCAGAAAAAAUCUGCUUGGUCGAAUCACCAUCGGAAAAUAUACUUAAUAGUAUAAU .....(((((.........((((((.........))))))...........(((((((.....)))))))(((......)))...))))).((((((....)))))).. (-18.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 68 27 91 51 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 298 68 23 150 103 NC_009009:SSA_0679|5end_DNA_repair_and_genetic_recombination,_putative_660714..660944_POSITIVE 277 77 31 98 52 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 259 69 23 177 118 NC_009009:SSA_1409|5end_DTDP-glucose-4,6-dehydratase,_putative_1422255..1422485_NEGATIVE 258 58 23 217 171 NC_009009:SSA_2055|5end_hypothetical_protein_2058160..2058390_NEGATIVE 254 65 27 211 167 NC_009009:SSA_0477|5end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_479223..479453_POSITIVE 249 68 23 207 159 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 249 57 21 58 14 NC_009009:SSA_1465|5end_Conserved_uncharacterized_protein_1471986..1472216_NEGATIVE 247 66 23 155 108 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 246 64 23 175 132 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 245 59 21 72 29 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 244 64 21 66 17 NC_009009:SSA_1854|5end_Conserved_uncharacterized_protein_1850884..1851114_NEGATIVE 239 58 13 219 161 NC_009009:SSA_1847|5end_RRNA_methyltransferase_RsmB,_putative_1842004..1842234_NEGATIVE 239 63 25 189 151 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 238 36 4 45 9 NC_009009:SSA_1296|5end_hypothetical_protein_1313013..1313243_NEGATIVE 238 67 24 231 190 NC_009009:SSA_0111|5end_30S_ribosomal_protein_S19,_putative_110672..110902_POSITIVE 237 61 21 58 3 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 235 69 24 46 3 NC_009009:SSA_1278|5end_Rhodanese-like_domain_protein,_putative_1299877..1300107_NEGATIVE 234 65 26 78 39 NC_009009:SSA_1385|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_1402268..1402498_POSITIVE 228 68 23 149 113 NC_009009:SSA_0996|5end_cGMP-specific_phosphodiesterase,_putative_996282..996512_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 68 23 141 94 NC_009009:SSA_0678|3end_Transcriptional_regulator,_ArgR_family,_putative_660785..660935_POSITIVE 273 76 31 98 46 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 271 87 41 123 85 NC_009009:SSA_0218|3end_Sugar-binding_periplasmic_protein,_putative_215226..215376_POSITIVE 270 57 14 126 83 NC_009009:SSA_1173|3end_Lipoate_protein_ligase_A,_putative_1200092..1200242_NEGATIVE 251 67 21 93 35 NC_009009:SSA_0513|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_512237..512387_POSITIVE 249 68 23 122 74 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 249 65 35 61 28 NC_009009:SSA_1615|3end_Alanine_dehydrogenase,_putative_1619318..1619468_POSITIVE 247 66 23 151 104 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 246 64 23 80 37 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 244 64 21 53 4 NC_009009:SSA_1855|3end_hypothetical_protein_1850897..1851047_NEGATIVE 242 69 22 53 1 NC_009009:SSA_1279|3end_Oxidoreductase,_putative_1299870..1300020_NEGATIVE 238 67 24 145 104 NC_009009:SSA_0110|3end_50S_ribosomal_protein_L2,_putative_110666..110816_POSITIVE 228 68 23 119 83 NC_009009:SSA_0995|3end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_996332..996482_POSITIVE 225 65 23 94 44 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 220 67 24 145 101 NC_009009:SSA_2174|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2171991..2172141_NEGATIVE 220 62 30 65 27 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 216 57 18 148 103 NC_009009:SSA_1628|3end_MutT/nudix_family_protein,_putative_1630363..1630513_POSITIVE 213 63 27 51 16 NC_009009:SSA_1415|3end_Oxidoreductase,_putative_1425414..1425564_NEGATIVE 208 57 25 39 1 NC_009009:SSA_1466|3end_Prephenate_dehydrogenase,_putative_1472005..1472155_NEGATIVE 207 68 22 91 42 NC_009009:SSA_2313|3end_hypothetical_protein_2315405..2315555_NEGATIVE