Origin IGS: taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggatattttttgcttttttatttgttttaagttaaaataaaccagt .........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 actggtttattttaacttaaaacaaataaaaaagcaaaaaatatccccagaattgctggaaaatgaataaaatgtaatataattgaaatattataaagcaaaaacaagacgttttgaaagctcaaaatgtcttgtttttttaagagtttagtcaagttgtggaagatggggagtgttggctaaatcctttttcttttctgaccta Mask Tandem Repeat Region ================================================ taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggatattttttgcttttttatttgttttaagttaaaataaaccagt Find is-nt database================================================ Query_seq: SSA_1523:SSA_1525|SSA_1523:SSA_1525:Glutathione peroxidase, putative:Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative:->->:1532681..1532885 205 taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggatattttttgcttttttatttgttttaagttaaaataaaccagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1523:SSA_1525|SSA_1523:SSA_1525:Glutathione peroxidase, putative:Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative:->->:1532681..1532885 205 taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggatattttttgcttttttatttgttttaagttaaaataaaccagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1523:SSA_1525|SSA_1523:SSA_1525:Glutathione peroxidase, putative:Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative:->->:1532681..1532885 205 taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggatattttttgcttttttatttgttttaagttaaaataaaccagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggatattttttgcttttttatttgttttaagttaaaataaaccagt Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 39 End: 191 ...................................... M F H N L T K L L K K Q D I L S F Q N V L F L L Y N I S I I L H F I H F P A I L G I F F A F L F V L S .............. taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggatattttttgcttttttatttgttttaagttaaaataaaccagt 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: 87 Start: 87 End: 116 ......................................................................................TTTCAAAACGTCTTGTTTTTGCTTTATAAT......................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 168 End: 197 .......................................................................................................................................................................TTTGCTTTTTTATTTGTTTTAAGTTAAAAT........ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggatattttttgcttttttatttgttttaagttaaaataaaccagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.9 Tail_Score: -5.05505 Start: 72 End: 101 Full_Region: AAACTCTTAAAAAAA CAAGACATTTTGA GCTT TCAAAACGTCTTG TTTTTGCTTTATAAT .......................................................................CAAGACATTTTGAGCTTTCAAAACGTCTTG........................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -13.1 Tail_Score: -5.4477 Start: 72 End: 101 Full_Region: attataaagcaaaaa caagacgttttga aagc tcaaaatgtcttg tttttttaagagttt .......................................................................caagacgttttgaaagctcaaaatgtcttg........................................................................................................ Find igs database================================================ Query_seq: SSA_1523:SSA_1525|SSA_1523:SSA_1525:Glutathione peroxidase, putative:Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative:->->:1532681..1532885 205 taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggatattttttgcttttttatttgttttaagttaaaataaaccagt Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: NC_009009_SSA_1523_SSA_1525|Glutathione peroxidase, putative:Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative|POSITIVE:POSITIVE|[1532681,1532885]|205 HSP 1 e-value: 1.0E-75 bit: 283.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttnnnnnnncaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggata......................................... taggtcagaaaagaaaaaggatttagccaacactccccatcttccacaacttgactaaactcttaaaaaaacaagacattttgagctttcaaaacgtcttgtttttgctttataatatttcaattatattacattttattcattttccagcaattctggggata......................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUCAGAAAAGAAAAAGGAUUUAGCCAACACUCCCCAUCUUCCACAACUUGACUAAACUCUUAAAAAAACAAGACAUUUUGAGCUUUCAAAACGUCUUGUUUUUGCUUUAUAAUAUUUCAAUUAUAUUACAUUUUAUUCAUUUUCCAGCAAUUCUGGGGAUA .......(((.((((.(((..(((((.(((....................))).)))))..)))..(((((((((((.(((((......))))).)))))))))))....((((((......)))))).....)))).)))..(..((((.....))))..).. (-30.45) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCCCCAGAAUUGCUGGAAAAUGAAUAAAAUGUAAUAUAAUUGAAAUAUUAUAAAGCAAAAACAAGACGUUUUGAAAGCUCAAAAUGUCUUGUUUUUUUAAGAGUUUAGUCAAGUUGUGGAAGAUGGGGAGUGUUGGCUAAAUCCUUUUUCUUUUCUGACCUA .....((((.....))))....(((((....((((((((.......))))))))....((((((((((((((((((....))))))))))))))))))......)))))((((.(....((((((.(((.(((....)))...))).))))))...)))))... (-40.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 120 75 119 71 NC_009009:SSA_0378|5end_TRZ/ATZ_family_hydrolase,_putative_367276..367506_POSITIVE 254 45 3 43 1 NC_009009:SSA_0406|5end_hypothetical_protein_402918..403148_NEGATIVE 253 44 5 79 42 NC_009009:SSA_0975|5end_2-isopropylmalate_synthase,_putative_980971..981201_POSITIVE 250 63 32 198 165 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 237 44 3 117 65 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 232 43 5 45 3 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 231 43 3 108 59 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 230 48 2 71 21 NC_009009:SSA_1916|5end_hypothetical_protein_1905487..1905717_POSITIVE 230 54 11 204 141 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 227 56 18 178 136 NC_009009:SSA_0568|5end_Aspartyl-tRNA_synthetase_1,_putative_561674..561904_POSITIVE 225 43 1 200 151 NC_009009:SSA_1345|5end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363879..1364109_NEGATIVE 225 54 12 219 172 NC_009009:SSA_0023|5end_Aspartate_aminotransferase,_putative_28529..28759_POSITIVE 224 42 18 228 199 NC_009009:SSA_0410|5end_hypothetical_protein_406442..406672_NEGATIVE 223 60 17 89 32 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 222 55 35 198 169 NC_009009:SSA_1939|5end_Acyl_carrier_protein,_putative_1926099..1926329_NEGATIVE 217 49 20 107 70 NC_009009:SSA_0246|5end_Conserved_uncharacterized_protein_239703..239933_POSITIVE 215 40 11 209 177 NC_009009:SSA_1748|5end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1734478..1734708_NEGATIVE 213 50 1 61 9 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 212 46 12 115 68 NC_009009:SSA_0655|5end_Cell_division_protein_FtsA,_putative_638784..639014_POSITIVE 210 110 80 172 137 NC_009009:SSA_1521|5end_Phosphoenolpyruvate_carboxylase,_putative_1530683..1530913_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 87 41 56 18 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 273 45 2 50 7 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 249 55 27 144 114 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 237 44 3 120 68 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 234 36 2 138 104 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 232 43 5 48 6 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 231 43 3 92 43 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 223 60 17 81 24 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 222 55 35 142 113 NC_009009:SSA_1940|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1926155..1926305_NEGATIVE 215 40 11 70 38 NC_009009:SSA_1749|3end_Pyruvate_formate-lyase-activating_enzyme,_putative_1734617..1734767_NEGATIVE 215 58 28 38 3 NC_009009:SSA_0829|3end_Platelet-binding_glycoprotein_812165..812315_POSITIVE 210 110 80 125 90 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 210 53 12 144 93 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 209 109 74 49 8 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE 208 46 1 87 47 NC_009009:SSA_0530|3end_Ethanolamine_utilization_protein_(transporter),_putative_527417..527567_POSITIVE 205 57 33 122 97 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 205 66 27 143 89 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 205 63 26 127 96 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 205 52 18 92 47 NC_009009:SSA_0297|3end_Malolactic_enzyme,_putative_291411..291561_POSITIVE 203 110 73 55 18 NC_009009:SSA_1762|3end_Permease,_putative_1748928..1749078_NEGATIVE