Origin IGS: cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg .........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 cagcatcctcctttatgaatctgacctagcctgcaacgacgcttgctatttattttcaatatataaacaaaaatccgaaaacagaatatttttcactatgttattaatattctataaacattataactatttttttgtactatgtcaacgcttacatttgagatttatagctttttttgatagtatagcagcagaggaaacaag Mask Tandem Repeat Region ================================================ cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg Find is-nt database================================================ Query_seq: SSA_0267:SSA_0268|SSA_0267:SSA_0268:ROK family protein, putative:Phosphotransferase system (PTS) cellobiose-specific component IIB, putative:<-->:262160..262363 204 cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0267:SSA_0268|SSA_0267:SSA_0268:ROK family protein, putative:Phosphotransferase system (PTS) cellobiose-specific component IIB, putative:<-->:262160..262363 204 cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0267:SSA_0268|SSA_0267:SSA_0268:ROK family protein, putative:Phosphotransferase system (PTS) cellobiose-specific component IIB, putative:<-->:262160..262363 204 cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: - Start: 3 End: 200 .. S D F F A I F R L H L R Q C L V F F Y N Y H K Y F I L L M T F F I R N E S K Q K Y I S F L Y C A D N C A L D S E Y L L M .... cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg 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: 92 Start: 56 End: 85 .......................................................GTTGACATAGTACAAAAAAATAGTTATAAT....................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 19 End: 48 ..................TTTGAGATTTATAGCTTTTTTTGATAGTAT............................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -2.2 Tail_Score: -5.4433 Start: 120 End: 131 Full_Region: CATAGTGAAAAATAT TCTG TTTT CGGA TTTTTGTTTATATAT .......................................................................................................................TCTGTTTTCGGA......................................................................... Find igs database================================================ Query_seq: SSA_0267:SSA_0268|SSA_0267:SSA_0268:ROK family protein, putative:Phosphotransferase system (PTS) cellobiose-specific component IIB, putative:<-->:262160..262363 204 cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg Intra-Species Hit: Count: 1 Min: 1 Max: 204 Len: 204 Subject: NC_009009_SSA_0267_SSA_0268|ROK family protein, putative:Phosphotransferase system (PTS) cellobiose-specific component IIB, putative|NEGATIVE:POSITIVE|[262160,262363]|204 HSP 1 e-value: 5.0E-87 bit: 321.0 Len: 204 Query Start:1 Query End:204 Subject Strand: POSITIVE Subject Start: 1 Subject End: 204 cttgtttcctctgctgctatactatcnnnnnnngctataaatctcaaatgtaagcgttgacatagtacnnnnnnntagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg cttgtttcctctgctgctatactatcaaaaaaagctataaatctcaaatgtaagcgttgacatagtacaaaaaaatagttataatgtttatagaatattaataacatagtgaaaaatattctgttttcggatttttgtttatatattgaaaataaatagcaagcgtcgttgcaggctaggtcagattcataaaggaggatgctg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUUUCCUCUGCUGCUAUACUAUCAAAAAAAGCUAUAAAUCUCAAAUGUAAGCGUUGACAUAGUACAAAAAAAUAGUUAUAAUGUUUAUAGAAUAUUAAUAACAUAGUGAAAAAUAUUCUGUUUUCGGAUUUUUGUUUAUAUAUUGAAAAUAAAUAGCAAGCGUCGUUGCAGGCUAGGUCAGAUUCAUAAAGGAGGAUGCUG ...((.((((((.(((((...............(((((.....(((((((((((((..((.................((((((((((((...))))))).)))))....((((((........))))))..))..))))))))).))))......)))))....(((......)))..)).))).........)))))).)).. (-35.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCAUCCUCCUUUAUGAAUCUGACCUAGCCUGCAACGACGCUUGCUAUUUAUUUUCAAUAUAUAAACAAAAAUCCGAAAACAGAAUAUUUUUCACUAUGUUAUUAAUAUUCUAUAAACAUUAUAACUAUUUUUUUGUACUAUGUCAACGCUUACAUUUGAGAUUUAUAGCUUUUUUUGAUAGUAUAGCAGCAGAGGAAACAAG .....(((((...........((((.((((..((......))..))))..................(((((((...(((((........))))).....(((((..................)))))....))))))).....))))..((((((..(..(((...........)))..)..))).)))....)))))...... (-28.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 60 11 151 102 NC_009009:SSA_0267|5end_ROK_family_protein,_putative_262069..262299_NEGATIVE 316 179 161 219 201 NC_009009:SSA_1737|5end_Cystathionine_gamma-synthase,_putative_1723778..1724008_NEGATIVE 278 198 152 185 132 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 271 47 7 54 8 NC_009009:SSA_2310|5end_hypothetical_protein_2313418..2313648_NEGATIVE 266 193 157 87 49 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 264 187 158 38 5 NC_009009:SSA_0816|5end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797445..797675_POSITIVE 262 200 160 49 8 NC_009009:SSA_1938|5end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1925738..1925968_NEGATIVE 262 199 158 77 27 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 262 199 152 56 3 NC_009009:SSA_0783|5end_Proton-translocating_ATPase,_F0_sector,_subunit_a,_putative_766815..767045_POSITIVE 261 184 158 64 41 NC_009009:SSA_0415|5end_Permease,_putative_410568..410798_POSITIVE 258 198 156 67 12 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 258 196 160 199 169 NC_009009:SSA_0141|5end_Copper_chaperone,_putative_136893..137123_POSITIVE 257 60 11 94 40 NC_009009:SSA_1078|5end_hypothetical_protein_1095742..1095972_POSITIVE 254 197 156 222 177 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 254 183 147 151 107 NC_009009:SSA_0606|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_594532..594762_NEGATIVE 253 199 157 162 127 NC_009009:SSA_0401|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_398462..398692_POSITIVE 253 170 121 198 141 NC_009009:SSA_0027|5end_Acyl_carrier_protein,_putative_31474..31704_POSITIVE 250 197 168 42 8 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 249 198 157 57 19 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 248 183 156 151 115 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 179 161 122 104 NC_009009:SSA_1738|3end_Polysaccharide_biosynthesis_protein,_putative_1723875..1724025_NEGATIVE 281 189 158 119 79 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 266 199 171 116 74 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 266 193 157 66 28 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 262 199 158 61 11 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 258 198 156 74 19 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 257 185 142 139 92 NC_009009:SSA_1398|3end_Membrane_protein,_hemolysin_III-like,_putative_1411626..1411776_POSITIVE 257 60 11 101 47 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 254 197 156 141 96 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE 254 183 147 93 49 NC_009009:SSA_0607|3end_ABC_transporter,_permease_component,_putative_594590..594740_NEGATIVE 248 194 158 39 1 NC_009009:SSA_0835|3end_Accessory_secretory_protein_Asp3,_putative_821595..821745_POSITIVE 248 199 160 49 6 NC_009009:SSA_0608|3end_Macrolide-efflux_protein,_putative_596901..597051_NEGATIVE 242 35 1 136 90 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 233 200 155 75 28 NC_009009:SSA_2282|3end_Phage_infection_protein,_putative_2282377..2282527_NEGATIVE 230 184 158 140 104 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 230 186 157 44 12 NC_009009:SSA_2090|3end_Hexulose-6-phosphate_synthase,_putative_2094343..2094493_NEGATIVE 229 199 161 145 110 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 225 188 146 144 110 NC_009009:SSA_1750|3end_Extracellular_nuclease,_putative_1735673..1735823_NEGATIVE 224 198 162 43 1 NC_009009:SSA_2118|3end_Thiamine_pyrophosphokinase,_putative_2119814..2119964_NEGATIVE 224 193 164 101 62 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE