Origin IGS: agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg .........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 caagcaaagttaactcttagaaaggatctaggagttttttctttattcgatacataaatgctcatttttgttggaaaaacaatcttatttttctaacaaaacatttttgtaaccaaattgtaataaaaaaaccattaaaaggatacgtttgctactagttaatactagtgttttgtgatagtatattact Mask Tandem Repeat Region ================================================ agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg Find is-nt database================================================ Query_seq: SSA_1301:SSA_1302|SSA_1301:SSA_1302:Conserved uncharacterized protein, possible surface protein:tRNA (Guanine-N(1)-)-methyltransferase, putative:<-<-:1321662..1321851 190 agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1301:SSA_1302|SSA_1301:SSA_1302:Conserved uncharacterized protein, possible surface protein:tRNA (Guanine-N(1)-)-methyltransferase, putative:<-<-:1321662..1321851 190 agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1301:SSA_1302|SSA_1301:SSA_1302:Conserved uncharacterized protein, possible surface protein:tRNA (Guanine-N(1)-)-methyltransferase, putative:<-<-:1321662..1321851 190 agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 5 End: 103 .... M Y Y H K T L V L T S S K R I L L M V F L L Q F G Y K N V L L E K ....................................................................................... Protein_Len: 37 Strand: - Start: 36 End: 146 ................................... Y C V Y G K L P K K I V I Q N C F H K T L F I L N N K W C F H A N I Y R M ............................................ agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg 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================================================ agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1301:SSA_1302|SSA_1301:SSA_1302:Conserved uncharacterized protein, possible surface protein:tRNA (Guanine-N(1)-)-methyltransferase, putative:<-<-:1321662..1321851 190 agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: NC_009009_SSA_1301_SSA_1302|Conserved uncharacterized protein, possible surface protein:tRNA (Guanine-N(1)-)-methyltransferase, putative|NEGATIVE:NEGATIVE|[1321662,1321851]|190 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggnnnnnnnattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg agtaatatactatcacaaaacactagtattaactagtagcaaacgtatccttttaatggtttttttattacaatttggttacaaaaatgttttgttagaaaaataagattgtttttccaacaaaaatgagcatttatgtatcgaataaagaaaaaactcctagatcctttctaagagttaactttgcttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAUAUACUAUCACAAAACACUAGUAUUAACUAGUAGCAAACGUAUCCUUUUAAUGGUUUUUUUAUUACAAUUUGGUUACAAAAAUGUUUUGUUAGAAAAAUAAGAUUGUUUUUCCAACAAAAAUGAGCAUUUAUGUAUCGAAUAAAGAAAAAACUCCUAGAUCCUUUCUAAGAGUUAACUUUGCUUG .((((((....((((......((((((....)))))).((....))..........)))).....)))))).(((((((.(((.((((((((((((.((((((((....)))))))).)))).....)))))))).))))))))))........(((((.((((.....)))).)))))........... (-38.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGCAAAGUUAACUCUUAGAAAGGAUCUAGGAGUUUUUUCUUUAUUCGAUACAUAAAUGCUCAUUUUUGUUGGAAAAACAAUCUUAUUUUUCUAACAAAACAUUUUUGUAACCAAAUUGUAAUAAAAAAACCAUUAAAAGGAUACGUUUGCUACUAGUUAAUACUAGUGUUUUGUGAUAGUAUAUUACU .....((((..((((((((((.....))))))))))....))))......((((.(((((.....((((((((((((((........))))))))))))))))))).))))........((((((......((.......)).((((...((.((((((....))))))))..))))......)))))). (-42.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 769 50 1 141 92 NC_009009:SSA_1301|5end_Conserved_uncharacterized_protein,_possible_surface_protein_1321571..1321801_NEGATIVE 261 190 154 218 186 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 245 189 157 132 98 NC_009009:SSA_0933|5end_Acetyltransferase,_GNAT_family,_putative_942734..942964_POSITIVE 235 68 36 117 81 NC_009009:SSA_0718|5end_Conserved_uncharacterized_protein_703761..703991_POSITIVE 223 167 127 66 22 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 207 188 147 210 172 NC_009009:SSA_1365|5end_FmtA-like_protein,_putative_1382299..1382529_NEGATIVE 202 79 32 207 156 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 202 188 156 150 110 NC_009009:SSA_1329|5end_Conserved_uncharacterized_protein_1345904..1346134_NEGATIVE 201 169 126 81 48 NC_009009:SSA_1915|5end_hypothetical_protein_1905440..1905670_NEGATIVE 198 46 1 86 38 NC_009009:SSA_0847|5end_6-phosphofructokinase,_putative_833372..833602_POSITIVE 195 188 158 139 107 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 195 135 100 177 141 NC_009009:SSA_0514|5end_PduQ_protein,_putative_512877..513107_POSITIVE 194 77 33 124 82 NC_009009:SSA_2059|5end_16S_rRNA_uridine-516_pseudouridylate_synthase,_putative_2061222..2061452_NEGATIVE 190 190 144 187 133 NC_009009:SSA_1168|5end_hypothetical_protein_1194151..1194381_POSITIVE 189 183 141 221 173 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 188 160 112 139 94 NC_009009:SSA_1406|5end_Histone_acetyltransferase_HPA2,_putative_1420315..1420545_NEGATIVE 187 118 77 76 32 NC_009009:SSA_0934|5end_HydD,_putative_943208..943438_POSITIVE 187 117 88 146 114 NC_009009:SSA_0865|5end_hypothetical_protein_856378..856608_POSITIVE 186 78 31 227 180 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 186 190 156 56 20 NC_009009:SSA_0776|5end_Glucose-1-phosphate_adenylyltransferase,_putative_758298..758528_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 190 154 102 70 NC_009009:SSA_2359|3end_Glucose_inhibited_division_protein_A,_putative_2360613..2360763_NEGATIVE 245 189 157 122 88 NC_009009:SSA_0932|3end_hypothetical_protein_942804..942954_POSITIVE 223 167 127 47 3 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 202 79 32 151 100 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 194 77 33 112 70 NC_009009:SSA_2060|3end_Arabinose_efflux_permease,_putative_2061234..2061384_NEGATIVE 193 60 13 130 80 NC_009009:SSA_2290|3end_hypothetical_protein_2292964..2293114_POSITIVE 190 190 144 127 73 NC_009009:SSA_1167|3end_SRP54,_signal_recognition_particle_GTPase_protein,_putative_1194171..1194321_POSITIVE 188 160 112 48 3 NC_009009:SSA_1408|3end_hypothetical_protein_1420406..1420556_NEGATIVE 187 118 77 45 1 NC_009009:SSA_0933|3end_Acetyltransferase,_GNAT_family,_putative_943257..943407_POSITIVE 186 78 31 105 58 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 186 190 156 49 13 NC_009009:SSA_0775|3end_1,4-alpha-glucan_branching_enzyme,_putative_758371..758521_POSITIVE 186 188 142 84 27 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 184 189 157 128 96 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 184 190 156 123 86 NC_009009:SSA_1257|3end_hypothetical_protein_1283106..1283256_NEGATIVE 184 79 37 149 114 NC_009009:SSA_1183|3end_hypothetical_protein_1210968..1211118_NEGATIVE 184 71 35 94 52 NC_009009:SSA_0366|3end_hypothetical_protein_358212..358362_POSITIVE 182 140 97 54 3 NC_009009:SSA_0684|3end_Fibril-like_structure_subunit_FibA,_putative_668893..669043_POSITIVE 180 190 157 110 75 NC_009009:SSA_0118|3end_50S_ribosomal_protein_L24,_putative_113748..113898_POSITIVE 179 179 157 119 88 NC_009009:SSA_1676|3end_Transcriptional_regulator,_LytTr_family,_putative_1670858..1671008_NEGATIVE 178 170 124 138 97 NC_009009:SSA_2029|3end_Transposase_and_inactivated_derivatives,_putative_2035633..2035783_NEGATIVE