Origin IGS: taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcacttctcctgagtaagatgttaatgataccattgtaacatactaaagattaaaaaacactattgataatttacaagtatatgacatttttcgttttatttcaaaaaatccaactcaaaaatgagttggatttaattcatatta Mask Tandem Repeat Region ================================================ taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct Find is-nt database================================================ Query_seq: SSA_1094:SSA_1095|SSA_1094:SSA_1095:GTP-binding protein, putative:Peptidoglycan hydrolase, putative:->->:1112304..1112449 146 taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1094:SSA_1095|SSA_1094:SSA_1095:GTP-binding protein, putative:Peptidoglycan hydrolase, putative:->->:1112304..1112449 146 taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1094:SSA_1095|SSA_1094:SSA_1095:GTP-binding protein, putative:Peptidoglycan hydrolase, putative:->->:1112304..1112449 146 taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct Predict ORF larger than 30AA ================================================ taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct 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: 40 End: 69 .......................................TTTGAAATAAAACGAAAAATGTCATATACT............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1094:SSA_1095|SSA_1094:SSA_1095:GTP-binding protein, putative:Peptidoglycan hydrolase, putative:->->:1112304..1112449 146 taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_009009_SSA_1094_SSA_1095|GTP-binding protein, putative:Peptidoglycan hydrolase, putative|POSITIVE:POSITIVE|[1112304,1112449]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct taatatgaattaaatccaactcatttttgagttggattttttgaaataaaacgaaaaatgtcatatacttgtaaattatcaatagtgttttttaatctttagtatgttacaatggtatcattaacatcttactcaggagaagtgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUGAAUUAAAUCCAACUCAUUUUUGAGUUGGAUUUUUUGAAAUAAAACGAAAAAUGUCAUAUACUUGUAAAUUAUCAAUAGUGUUUUUUAAUCUUUAGUAUGUUACAAUGGUAUCAUUAACAUCUUACUCAGGAGAAGUGCU ..((((((.....((((((((((....))))))))))((((((........))))))...)))))).................((..((((((.......((.((((((..(((....))))))))))).......))))))..)) (-30.34) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCACUUCUCCUGAGUAAGAUGUUAAUGAUACCAUUGUAACAUACUAAAGAUUAAAAAACACUAUUGAUAAUUUACAAGUAUAUGACAUUUUUCGUUUUAUUUCAAAAAAUCCAACUCAAAAAUGAGUUGGAUUUAAUUCAUAUUA ............((((((((((..((((.(((....)))..(((((..((((((..((......))..))))))...)))))....))))...))))))))))....((((((((((((....))))))))))))........... (-26.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 58 14 54 8 NC_009009:SSA_0708|5end_hypothetical_protein_694144..694374_POSITIVE 222 140 95 155 109 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 214 44 16 194 165 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 206 133 96 104 65 NC_009009:SSA_1213|5end_Pyridoxal-phosphate_dependent_aminotransferase,_putative_1236290..1236520_POSITIVE 205 139 96 212 169 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 200 93 51 84 39 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 197 136 95 146 106 NC_009009:SSA_2248|5end_hypothetical_protein_2243809..2244039_NEGATIVE 190 36 5 112 75 NC_009009:SSA_0402|5end_Histidine_kinase,_putative_399144..399374_POSITIVE 185 135 97 90 50 NC_009009:SSA_1344|5end_Xanthine/uracil_permeases,_putative_1363352..1363582_NEGATIVE 180 40 15 214 188 NC_009009:SSA_1406|5end_Histone_acetyltransferase_HPA2,_putative_1420315..1420545_NEGATIVE 180 136 110 75 49 NC_009009:SSA_1194|5end_Aspartate-semialdehyde_dehydrogenase,_putative_1221189..1221419_NEGATIVE 180 74 31 88 45 NC_009009:SSA_0480|5end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_481162..481392_POSITIVE 179 140 92 163 111 NC_009009:SSA_1946|5end_Oligopeptide_transport_system_permease_protein,_putative_1938624..1938854_NEGATIVE 179 136 96 230 188 NC_009009:SSA_0368|5end_hypothetical_protein_359274..359504_POSITIVE 178 57 20 151 107 NC_009009:SSA_1180|5end_hypothetical_protein_1208559..1208789_NEGATIVE 168 69 21 215 150 NC_009009:SSA_1685|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1679076..1679306_NEGATIVE 166 139 106 88 45 NC_009009:SSA_2088|5end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2093476..2093706_NEGATIVE 165 118 71 212 169 NC_009009:SSA_0587|5end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_578539..578769_POSITIVE 164 44 15 130 99 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 162 44 13 168 128 NC_009009:SSA_1582|5end_Esterase,_alpha/beta_hydrolase_superfamily,_putative_1584671..1584901_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 39 12 79 52 NC_009009:SSA_1094|3end_GTP-binding_protein,_putative_1112243..1112393_POSITIVE 214 44 16 125 96 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 197 136 95 149 109 NC_009009:SSA_2249|3end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_2243806..2243956_NEGATIVE 194 47 5 125 76 NC_009009:SSA_1106|3end_IgA-specific_metalloendopeptidase_1131678..1131828_POSITIVE 190 36 5 110 73 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 188 129 84 101 47 NC_009009:SSA_0914|3end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_927437..927587_POSITIVE 185 135 97 81 41 NC_009009:SSA_1345|3end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363361..1363511_NEGATIVE 180 40 15 123 97 NC_009009:SSA_1408|3end_hypothetical_protein_1420406..1420556_NEGATIVE 179 117 78 107 69 NC_009009:SSA_0888|3end_Magnesium/cobalt_transporter,_putative_882749..882899_POSITIVE 178 57 20 118 74 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE 178 42 3 78 42 NC_009009:SSA_1173|3end_Lipoate_protein_ligase_A,_putative_1200092..1200242_NEGATIVE 171 44 12 69 31 NC_009009:SSA_2205|3end_Transcription_antitermination_factor_NusG,_putative_2205564..2205714_NEGATIVE 166 139 106 88 45 NC_009009:SSA_2089|3end_L-xylulose-5-phosphate_3-epimerase,_putative_2093476..2093626_NEGATIVE 164 44 15 149 118 NC_009009:SSA_1252|3end_hypothetical_protein_1276771..1276921_NEGATIVE 162 139 110 84 41 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 161 140 93 151 108 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE 159 140 96 103 59 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 159 39 7 91 55 NC_009009:SSA_1876|3end_hypothetical_protein_1871742..1871892_POSITIVE 159 139 96 79 35 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE 158 108 61 127 63 NC_009009:SSA_1514|3end_Cell-wall_biogenesis_glycosyltransferase,_putative_1521001..1521151_NEGATIVE