Origin IGS: ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc .........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 gatgacttctcctttatattttaaaatttacttccttagtttactcctaaaatatcaaatagtcaatcttttgccaccattgtaagcgttttttgtttcattcttttgatttataaattttcctgtcaaaacaattgaattattattgatatacaaactattctgctatataaataagaagaaagcgattaaaatttcacttatttcatatattttttaaagaaaaaagagcaaagtgattatttgctcttgattttcctatag Mask Tandem Repeat Region ================================================ ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc Find is-nt database================================================ Query_seq: SSA_0781:SSA_0782|SSA_0781:SSA_0782:Mannose-6-phosphate isomerase, putative:Proton-translocating ATPase, F0 sector, subunit c, putative:->->:766455..766718 264 ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0781:SSA_0782|SSA_0781:SSA_0782:Mannose-6-phosphate isomerase, putative:Proton-translocating ATPase, F0 sector, subunit c, putative:->->:766455..766718 264 ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0781:SSA_0782|SSA_0781:SSA_0782:Mannose-6-phosphate isomerase, putative:Proton-translocating ATPase, F0 sector, subunit c, putative:->->:766455..766718 264 ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 109 End: 207 ............................................................................................................ M Y I N N N S I V L T G K F I N Q K N E T K N A Y N G G K R L T I ......................................................... Protein_Len: 35 Strand: - Start: 48 End: 152 ............................................... F I Y S I L S I K I A K K K N I Y C F L K Y I L L L E I T K V P F N M ................................................................................................................ ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc 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: 198 End: 227 .....................................................................................................................................................................................................ATTGACTATTTGATATTTTAGGAGTAAACT..................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 91 End: 120 ..........................................................................................ATTGATATACAAACTATTCTGCTATATAAA................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 43 HP_score: -2.3 Tail_Score: -3.44148 Start: 18 End: 34 Full_Region: tttaaagaaaaaaga gcaaa gtgatta tttgc tcttgattttcctat .................gcaaagtgattatttgc...................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0781:SSA_0782|SSA_0781:SSA_0782:Mannose-6-phosphate isomerase, putative:Proton-translocating ATPase, F0 sector, subunit c, putative:->->:766455..766718 264 ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc Intra-Species Hit: Count: 1 Min: 1 Max: 264 Len: 264 Subject: NC_009009_SSA_0781_SSA_0782|Mannose-6-phosphate isomerase, putative:Proton-translocating ATPase, F0 sector, subunit c, putative|POSITIVE:POSITIVE|[766455,766718]|264 HSP 1 e-value: 1.0E-148 bit: 523.0 Len: 264 Query Start:1 Query End:264 Subject Strand: POSITIVE Subject Start: 1 Subject End: 264 ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc ctataggaaaatcaagagcaaataatcactttgctcttttttctttaaaaaatatatgaaataagtgaaattttaatcgctttcttcttatttatatagcagaatagtttgtatatcaataataattcaattgttttgacaggaaaatttataaatcaaaagaatgaaacaaaaaacgcttacaatggtggcaaaagattgactatttgatattttaggagtaaactaaggaagtaaattttaaaatataaaggagaagtcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUAGGAAAAUCAAGAGCAAAUAAUCACUUUGCUCUUUUUUCUUUAAAAAAUAUAUGAAAUAAGUGAAAUUUUAAUCGCUUUCUUCUUAUUUAUAUAGCAGAAUAGUUUGUAUAUCAAUAAUAAUUCAAUUGUUUUGACAGGAAAAUUUAUAAAUCAAAAGAAUGAAACAAAAAACGCUUACAAUGGUGGCAAAAGAUUGACUAUUUGAUAUUUUAGGAGUAAACUAAGGAAGUAAAUUUUAAAAUAUAAAGGAGAAGUCAUC ....(((((((..(((((((((.......))))))))))))))))..........((((...((((((........)))))).((((((.(((((((....((((((((.....(((........((((.((.((((((................)))))).))))))........((((......))))......))).))))))))..((((((...((....))...)))))).........))))))).)))))))))). (-46.39) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGACUUCUCCUUUAUAUUUUAAAAUUUACUUCCUUAGUUUACUCCUAAAAUAUCAAAUAGUCAAUCUUUUGCCACCAUUGUAAGCGUUUUUUGUUUCAUUCUUUUGAUUUAUAAAUUUUCCUGUCAAAACAAUUGAAUUAUUAUUGAUAUACAAACUAUUCUGCUAUAUAAAUAAGAAGAAAGCGAUUAAAAUUUCACUUAUUUCAUAUAUUUUUUAAAGAAAAAAGAGCAAAGUGAUUAUUUGCUCUUGAUUUUCCUAUAG (((((((........((((((((......(((.....))).......)))))))).....)))).)))...........(((((..((......((((.(((.(((((((..............))))))).))).))))......))...))))).........(((((.......((((.(((.((........)).))).))))..............((((((((((((((.......)))))))))..))))).))))) (-35.58) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 47 1 190 141 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 273 112 71 157 117 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 241 110 64 169 117 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 238 127 83 62 22 NC_009009:SSA_2221|5end_Cps9E,_putative_2223257..2223487_NEGATIVE 236 55 14 77 36 NC_009009:SSA_1337|5end_hypothetical_protein_1351091..1351321_NEGATIVE 235 124 81 139 97 NC_009009:SSA_0615|5end_RggD,_putative_609195..609425_NEGATIVE 224 210 170 71 29 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 222 113 76 126 92 NC_009009:SSA_0918|5end_Conserved_uncharacterized_protein_930398..930628_POSITIVE 216 210 169 37 2 NC_009009:SSA_0718|5end_Conserved_uncharacterized_protein_703761..703991_POSITIVE 216 39 1 217 181 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 216 232 193 205 153 NC_009009:SSA_0401|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_398462..398692_POSITIVE 214 103 61 138 90 NC_009009:SSA_1358|5end_hypothetical_protein_1374036..1374266_NEGATIVE 212 123 81 142 97 NC_009009:SSA_2283|5end_Conserved_uncharacterized_protein_2285824..2286054_NEGATIVE 212 45 4 62 17 NC_009009:SSA_0461|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_463059..463289_POSITIVE 207 118 79 139 94 NC_009009:SSA_0101|5end_Conserved_uncharacterized_protein_103596..103826_POSITIVE 206 52 19 110 76 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 202 204 165 170 127 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 202 227 186 42 10 NC_009009:SSA_0407|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_403843..404073_NEGATIVE 200 199 155 194 141 NC_009009:SSA_1727|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713420..1713650_NEGATIVE 200 223 183 219 179 NC_009009:SSA_1005|5end_Sugar_ABC_transporter,_permease_protein,_putative_1006028..1006258_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 47 1 113 64 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 273 112 71 79 39 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 224 210 170 60 18 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 221 45 5 86 46 NC_009009:SSA_0781|3end_Mannose-6-phosphate_isomerase,_putative_766394..766544_POSITIVE 212 45 4 69 24 NC_009009:SSA_0460|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_463146..463296_POSITIVE 206 52 19 62 28 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 204 47 16 121 83 NC_009009:SSA_2201|3end_hypothetical_protein_2202237..2202387_POSITIVE 202 44 14 67 29 NC_009009:SSA_0584|3end_hypothetical_protein_576689..576839_POSITIVE 199 36 1 101 62 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 196 80 34 145 97 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 195 118 84 39 1 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 195 192 151 73 38 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 194 220 178 57 22 NC_009009:SSA_0053|3end_Beta-galactosidase,_putative_58615..58765_POSITIVE 193 107 67 56 19 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 193 90 49 106 56 NC_009009:SSA_1921|3end_hypothetical_protein_1911317..1911467_POSITIVE 193 110 77 70 31 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 193 220 177 96 54 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 192 102 78 50 25 NC_009009:SSA_2209|3end_Penicillin-binding_protein_2A,_putative_2208144..2208294_NEGATIVE 190 117 84 36 1 NC_009009:SSA_1196|3end_Acetyltransferase,_GNAT_family,_putative_1221528..1221678_NEGATIVE 190 229 188 84 43 NC_009009:SSA_1135|3end_Na+-driven_multidrug_efflux_pump,_putative_1161775..1161925_POSITIVE