Origin IGS: aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa .........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 ttcttactctccttattatttaaaattatttactagtctatgatacctcaaaaacgcttttttttcaaggaaaaatagagaatctaagcaaatttgagaaattttgcacaagaaaacgattccaaatttactatataaatgtttttccggcaaatcagaaagaagattcgaccttttagaatttctccttttatggtacaattttatt Mask Tandem Repeat Region ================================================ aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa Find is-nt database================================================ Query_seq: SSA_0885:SSA_0886|SSA_0885:SSA_0886:hypothetical protein:Enolase, putative:<-->:879605..879812 208 aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0885:SSA_0886|SSA_0885:SSA_0886:hypothetical protein:Enolase, putative:<-->:879605..879812 208 aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0885:SSA_0886|SSA_0885:SSA_0886:hypothetical protein:Enolase, putative:<-->:879605..879812 208 aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 15 End: 122 .............. M K G E I L K G R I F F L I C R K N I Y I V N L E S F S C A K F L K F A ...................................................................................... Protein_Len: 60 Strand: + Start: 2 End: 190 . M K L Y H K R R N S K R S N L L S D L P E K H L Y S K F G I V F L C K I S Q I C L D S L F F L E K K A F L R Y H R L V N .................. Protein_Len: 34 Strand: - Start: 33 End: 134 ................................ F T S D E K Q N A P F V N I Y Y I Q F R K R T C F K E F K S L N E M .......................................................................... Protein_Len: 36 Strand: - Start: 1 End: 108 I F N Y W L L L F E L L D F R R E S K G S F C K Y L L N P I T K K H L M .................................................................................................... aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa 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: 90 Start: 140 End: 169 ...........................................................................................................................................CTTGAAAAAAAAGCGTTTTTGAGGTATCAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0885:SSA_0886|SSA_0885:SSA_0886:hypothetical protein:Enolase, putative:<-->:879605..879812 208 aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: NC_009009_SSA_0885_SSA_0886|hypothetical protein:Enolase, putative|NEGATIVE:POSITIVE|[879605,879812]|208 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 208 Query Start:1 Query End:208 Subject Strand: POSITIVE Subject Start: 1 Subject End: 208 aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgnnnnnnnngcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa aataaaattgtaccataaaaggagaaattctaaaaggtcgaatcttctttctgatttgccggaaaaacatttatatagtaaatttggaatcgttttcttgtgcaaaatttctcaaatttgcttagattctctatttttccttgaaaaaaaagcgtttttgaggtatcatagactagtaaataattttaaataataaggagagtaagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAAUUGUACCAUAAAAGGAGAAAUUCUAAAAGGUCGAAUCUUCUUUCUGAUUUGCCGGAAAAACAUUUAUAUAGUAAAUUUGGAAUCGUUUUCUUGUGCAAAAUUUCUCAAAUUUGCUUAGAUUCUCUAUUUUUCCUUGAAAAAAAAGCGUUUUUGAGGUAUCAUAGACUAGUAAAUAAUUUUAAAUAAUAAGGAGAGUAAGAA ....................((((((..((((...((.((((((........))))))))................(((((((((((((..((((((....).)))))))).))))))))))))))))))))..(((((((((..........((((.(((....))).))))...((((....)))).....)))))))))...... (-38.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUACUCUCCUUAUUAUUUAAAAUUAUUUACUAGUCUAUGAUACCUCAAAAACGCUUUUUUUUCAAGGAAAAAUAGAGAAUCUAAGCAAAUUUGAGAAAUUUUGCACAAGAAAACGAUUCCAAAUUUACUAUAUAAAUGUUUUUCCGGCAAAUCAGAAAGAAGAUUCGACCUUUUAGAAUUUCUCCUUUUAUGGUACAAUUUUAUU ....................(((((((...(((((...........((((((...((((..(((((...........)))))...))))...))))))....(((((....(((((((.....................)))))))...)))))...(((((.((((((.........)))..))).))))).))))).))))))).. (-25.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 70 21 161 112 NC_009009:SSA_0885|5end_hypothetical_protein_879514..879744_NEGATIVE 259 50 7 157 121 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 258 63 36 225 199 NC_009009:SSA_1086|5end_TRNA_nucleotidyltransferase,_putative_1103328..1103558_POSITIVE 256 141 101 111 80 NC_009009:SSA_0316|5end_hypothetical_protein_310576..310806_POSITIVE 247 105 74 214 183 NC_009009:SSA_1479|5end_Transposase,_putative_1483180..1483410_POSITIVE 246 146 108 50 1 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 244 100 60 218 176 NC_009009:SSA_0858|5end_DTDP-L-rhamnose_synthase,_putative_845512..845742_POSITIVE 240 64 21 119 72 NC_009009:SSA_1568|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571200..1571430_POSITIVE 236 126 86 73 38 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 231 62 38 120 99 NC_009009:SSA_1323|5end_hypothetical_protein_1340450..1340680_NEGATIVE 229 69 22 54 1 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 229 140 91 210 157 NC_009009:SSA_0023|5end_Aspartate_aminotransferase,_putative_28529..28759_POSITIVE 228 140 92 179 135 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 227 149 117 160 127 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 225 49 7 172 119 NC_009009:SSA_0988|5end_TfoX_N-terminal_domain_family_protein,_putative_990662..990892_POSITIVE 223 167 123 61 18 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 222 78 35 58 11 NC_009009:SSA_2120|5end_GTPase,_putative_2121751..2121981_NEGATIVE 222 68 23 196 149 NC_009009:SSA_1642|5end_N-acetylglucosamine-1-phosphate_uridyltransferase,_putative_1644482..1644712_NEGATIVE 222 132 97 228 205 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 222 100 54 65 23 NC_009009:SSA_0393|5end_Bacteriocin_ABC-type_exporter,_ATP_binding/permease_protein,_putative_388766..388996_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 128 83 103 56 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE 282 65 35 121 88 NC_009009:SSA_0445|3end_hypothetical_protein_444776..444926_POSITIVE 259 50 7 86 50 NC_009009:SSA_1920|3end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1910884..1911034_POSITIVE 256 141 101 101 70 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE 244 100 60 108 66 NC_009009:SSA_0857|3end_hypothetical_protein_845482..845632_POSITIVE 243 70 21 126 58 NC_009009:SSA_2022|3end_Transcriptional_regulator,_MerR_family_(multidrug-efflux_transporter_genes),_putative_2024488..2024638_POSITIVE 240 64 21 106 59 NC_009009:SSA_1567|3end_Polar_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_1571267..1571417_POSITIVE 236 126 86 69 34 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 231 62 38 142 121 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 228 154 116 49 11 NC_009009:SSA_0442|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_443030..443180_POSITIVE 227 149 117 81 48 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 222 68 23 68 21 NC_009009:SSA_1643|3end_hypothetical_protein_1644610..1644760_NEGATIVE 219 165 126 72 42 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 214 130 83 149 113 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 212 160 111 151 106 NC_009009:SSA_0366|3end_hypothetical_protein_358212..358362_POSITIVE 211 122 89 72 36 NC_009009:SSA_2036|3end_Conserved_hypothetical_cytosolic_protein_2040278..2040428_NEGATIVE 210 58 21 60 13 NC_009009:SSA_0080|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_84194..84344_POSITIVE 208 58 18 65 23 NC_009009:SSA_1086|3end_TRNA_nucleotidyltransferase,_putative_1104607..1104757_POSITIVE 205 64 33 116 76 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 204 140 91 72 23 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE