Origin IGS: tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttggttacgacctttcttatgaaatttaatttatttctttcgtaactattgtaacatgcaaaattctagaattcaatcatttataggcgattactgaattaaagattttttgcacatttgtgccatccgagccaagaaacttttgtgtttttatccatcaaaatcaga Mask Tandem Repeat Region ================================================ tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa Find is-nt database================================================ Query_seq: SSA_0284:SSA_0285|SSA_0284:SSA_0285:Phosphotransferase system (PTS), cellobiose-specific IIC component, putative:Formate acetyltransferase 3, putative:->->:276330..276497 168 tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0284:SSA_0285|SSA_0284:SSA_0285:Phosphotransferase system (PTS), cellobiose-specific IIC component, putative:Formate acetyltransferase 3, putative:->->:276330..276497 168 tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0284:SSA_0285|SSA_0284:SSA_0285:Phosphotransferase system (PTS), cellobiose-specific IIC component, putative:Formate acetyltransferase 3, putative:->->:276330..276497 168 tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa Predict ORF larger than 30AA ================================================ tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa 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: 85 Start: 92 End: 121 ...........................................................................................ATTGAATTCTAGAATTTTGCATGTTACAAT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0284:SSA_0285|SSA_0284:SSA_0285:Phosphotransferase system (PTS), cellobiose-specific IIC component, putative:Formate acetyltransferase 3, putative:->->:276330..276497 168 tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: NC_009009_SSA_0284_SSA_0285|Phosphotransferase system (PTS), cellobiose-specific IIC component, putative:Formate acetyltransferase 3, putative|POSITIVE:POSITIVE|[276330,276497]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa tctgattttgatggataaaaacacaaaagtttcttggctcggatggcacaaatgtgcaaaaaatctttaattcagtaatcgcctataaatgattgaattctagaattttgcatgttacaatagttacgaaagaaataaattaaatttcataagaaaggtcgtaaccaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUGAUUUUGAUGGAUAAAAACACAAAAGUUUCUUGGCUCGGAUGGCACAAAUGUGCAAAAAAUCUUUAAUUCAGUAAUCGCCUAUAAAUGAUUGAAUUCUAGAAUUUUGCAUGUUACAAUAGUUACGAAAGAAAUAAAUUAAAUUUCAUAAGAAAGGUCGUAACCAA .....(((((.((........)))))))..((((((..((((((......(((((((((((..(((..((((((((...............))))))))..))).)))))))))))......))).)))..(((((.......))))).)))))).(((....))).. (-28.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGGUUACGACCUUUCUUAUGAAAUUUAAUUUAUUUCUUUCGUAACUAUUGUAACAUGCAAAAUUCUAGAAUUCAAUCAUUUAUAGGCGAUUACUGAAUUAAAGAUUUUUUGCACAUUUGUGCCAUCCGAGCCAAGAAACUUUUGUGUUUUUAUCCAUCAAAAUCAGA .(((((((((..........(((((.......)))))..))))))))).((..((((((((((.(((..(((((((((..........)))...))))))..)))..)))))))....)))..))...((....((((((......)))))).....))......... (-26.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 47 2 191 140 NC_009009:SSA_0032|5end_Phosphoribosylformylglycinamidine_cyclo-ligase,_putative_37938..38168_POSITIVE 262 74 33 86 42 NC_009009:SSA_1223|5end_30S_ribosomal_protein_S1,_putative_1246872..1247102_NEGATIVE 260 57 30 169 144 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 245 50 9 69 31 NC_009009:SSA_1826|5end_Glycerol_kinase,_putative_1814536..1814766_POSITIVE 235 70 29 69 19 NC_009009:SSA_0602|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_589918..590148_POSITIVE 232 47 11 157 123 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 229 69 35 90 55 NC_009009:SSA_0233|5end_Permease,_putative_227203..227433_POSITIVE 228 57 31 49 23 NC_009009:SSA_0370|5end_Acetyltransferase,_GNAT_family,_putative_360382..360612_NEGATIVE 227 115 71 56 5 NC_009009:SSA_1812|5end_Modification_methylase,_putative_1798334..1798564_NEGATIVE 225 77 32 62 13 NC_009009:SSA_1668|5end_NrdI_protein,_putative_1668091..1668321_NEGATIVE 220 47 2 228 178 NC_009009:SSA_1430|5end_Ribonuclease_Z,_putative_1438036..1438266_NEGATIVE 220 46 8 57 10 NC_009009:SSA_0103|5end_Integral_membrane_protein,_putative_105490..105720_NEGATIVE 219 49 1 118 56 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 218 57 12 159 104 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 217 59 13 197 143 NC_009009:SSA_0730|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_714818..715048_POSITIVE 216 79 32 166 120 NC_009009:SSA_2089|5end_L-xylulose-5-phosphate_3-epimerase,_putative_2094339..2094569_NEGATIVE 215 83 41 89 58 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 214 80 31 156 99 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 214 57 31 227 204 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 213 77 32 199 144 NC_009009:SSA_0873|5end_ATP-dependent_DNA_helicase;_DNA_polymerase_III,_epsilon_subunit,_putative_865391..865621_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 47 6 126 82 NC_009009:SSA_1972|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1967811..1967961_NEGATIVE 265 47 2 131 80 NC_009009:SSA_0031|3end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_37958..38108_POSITIVE 235 70 29 59 9 NC_009009:SSA_0601|3end_Phosphorylase,_Pnp/Udp_family,_putative_589988..590138_POSITIVE 232 47 11 137 103 NC_009009:SSA_2335|3end_D-Ala-teichoic_acid_biosynthesis_protein,_putative_2338027..2338177_NEGATIVE 229 69 35 84 49 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 225 47 5 73 29 NC_009009:SSA_2024|3end_hypothetical_protein_2029105..2029255_NEGATIVE 225 77 32 58 9 NC_009009:SSA_1669|3end_hypothetical_protein_1668095..1668245_NEGATIVE 221 58 26 149 103 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 220 48 5 38 2 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 218 57 12 116 61 NC_009009:SSA_1541|3end_Peptidase,_U32_family,_putative_1545311..1545461_NEGATIVE 216 68 30 145 110 NC_009009:SSA_0218|3end_Sugar-binding_periplasmic_protein,_putative_215226..215376_POSITIVE 215 47 3 72 32 NC_009009:SSA_1052|3end_hypothetical_protein_1066846..1066996_NEGATIVE 215 83 41 102 71 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 209 82 41 149 95 NC_009009:SSA_0781|3end_Mannose-6-phosphate_isomerase,_putative_766394..766544_POSITIVE 208 126 81 133 94 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 207 69 28 68 20 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 204 58 28 131 98 NC_009009:SSA_1678|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1671336..1671486_NEGATIVE 202 68 25 91 56 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 201 57 36 18 1 NC_009009:SSA_0371|3end_NADP-specific_glutamate_dehydrogenase,_putative_360413..360563_NEGATIVE 199 45 6 62 22 NC_009009:SSA_2314|3end_hypothetical_protein_2315886..2316036_NEGATIVE