Origin IGS: gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaactctccttatttcaaactgtgattgtacttgaaatttattacatcctttcccattataccctatacccttatagtctgcaatatttttccaaactttggctgtaacagctgattctgatagccatttccataaaaaaatggtatcattaatctc Mask Tandem Repeat Region ================================================ gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt Find is-nt database================================================ Query_seq: SSA_0712:SSA_0713|SSA_0712:SSA_0713:P-type ATPase-metal cation transport (calcium efflux), putative:1-acyl-sn-glycerol-3-phosphate acyltransferase, putative:<-->:699191..699347 157 gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0712:SSA_0713|SSA_0712:SSA_0713:P-type ATPase-metal cation transport (calcium efflux), putative:1-acyl-sn-glycerol-3-phosphate acyltransferase, putative:<-->:699191..699347 157 gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0712:SSA_0713|SSA_0712:SSA_0713:P-type ATPase-metal cation transport (calcium efflux), putative:1-acyl-sn-glycerol-3-phosphate acyltransferase, putative:<-->:699191..699347 157 gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 4 End: 156 ... M N D T I F L W K W L S E S A V T A K V W K N I A D Y K G I G Y N G K G C N K F Q V Q S Q F E I R R V . gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt 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: 73 End: 102 ........................................................................ATTGCAGACTATAAGGGTATAGGGTATAAT....................................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 8 End: 37 .......ATAGCCATTTCCATAAAAAAATGGTATCAT........................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 98 End: 127 .................................................................................................CTTGAAATTTATTACATCCTTTCCCATTAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0712:SSA_0713|SSA_0712:SSA_0713:P-type ATPase-metal cation transport (calcium efflux), putative:1-acyl-sn-glycerol-3-phosphate acyltransferase, putative:<-->:699191..699347 157 gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_009009_SSA_0712_SSA_0713|P-type ATPase-metal cation transport (calcium efflux), putative:1-acyl-sn-glycerol-3-phosphate acyltransferase, putative|NEGATIVE:POSITIVE|[699191,699347]|157 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 gagattaatgataccannnnnnnatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt gagattaatgataccatttttttatggaaatggctatcagaatcagctgttacagccaaagtttggaaaaatattgcagactataagggtatagggtataatgggaaaggatgtaataaatttcaagtacaatcacagtttgaaataaggagagttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUUAAUGAUACCAUUUUUUUAUGGAAAUGGCUAUCAGAAUCAGCUGUUACAGCCAAAGUUUGGAAAAAUAUUGCAGACUAUAAGGGUAUAGGGUAUAAUGGGAAAGGAUGUAAUAAAUUUCAAGUACAAUCACAGUUUGAAAUAAGGAGAGUUU ..((((..(((((((((((((....)))))))).))))).))))...(((((((.((...((((....))))..(((...(((((....))))).)))..........)).))))))).((((((((...........))))))))........... (-30.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUCUCCUUAUUUCAAACUGUGAUUGUACUUGAAAUUUAUUACAUCCUUUCCCAUUAUACCCUAUACCCUUAUAGUCUGCAAUAUUUUUCCAAACUUUGGCUGUAACAGCUGAUUCUGAUAGCCAUUUCCAUAAAAAAAUGGUAUCAUUAAUCUC .......................(((((.....((((..((((.((..((.......((((...)))).......))..)).))))..))))......(..((((...))))..)...(((((.((((((........))))))))))).))))).. (-19.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 80 31 171 122 NC_009009:SSA_0712|5end_P-type_ATPase-metal_cation_transport_(calcium_efflux),_putative_699100..699330_NEGATIVE 309 89 46 173 137 NC_009009:SSA_1934|5end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921800..1922030_NEGATIVE 298 66 25 57 23 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 296 58 15 132 94 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 292 57 14 56 15 NC_009009:SSA_0370|5end_Acetyltransferase,_GNAT_family,_putative_360382..360612_NEGATIVE 287 60 11 76 13 NC_009009:SSA_2046|5end_Uridine_phosphorylase,_putative_2049721..2049951_NEGATIVE 279 78 35 225 182 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 275 58 14 50 4 NC_009009:SSA_1137|5end_Dihydrolipoamide_dehydrogenase,_putative_1164375..1164605_POSITIVE 274 89 42 217 154 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 273 62 25 223 186 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 272 90 45 173 135 NC_009009:SSA_0050|5end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_54612..54842_POSITIVE 261 57 25 64 28 NC_009009:SSA_0323|5end_Flavoprotein,_putative_316799..317029_NEGATIVE 259 56 16 220 178 NC_009009:SSA_0646|5end_hypothetical_protein_630778..631008_POSITIVE 258 67 21 63 11 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 258 88 45 44 2 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 256 108 62 223 165 NC_009009:SSA_1457|5end_Neopullulanase,_putative_1464239..1464469_NEGATIVE 254 67 21 58 9 NC_009009:SSA_0424|5end_Exopolysaccharide_biosynthesis_protein,_putative_422233..422463_NEGATIVE 254 58 14 59 13 NC_009009:SSA_0040|5end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_46308..46538_POSITIVE 248 67 26 51 5 NC_009009:SSA_1913|5end_Xanthine/uracil_permease_family_protein,_putative_1904666..1904896_NEGATIVE 248 48 1 193 140 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 139 92 101 39 NC_009009:SSA_1457|3end_Neopullulanase,_putative_1462485..1462635_NEGATIVE 263 60 13 62 1 NC_009009:SSA_2047|3end_hypothetical_protein_2049735..2049885_NEGATIVE 259 56 16 127 85 NC_009009:SSA_0644|3end_DNA_Protection_System,_DNA-binding_ferritin-like_protein_(oxidative_damage_protectant),_putative_630765..630915_POSITIVE 255 66 32 141 114 NC_009009:SSA_0049|3end_Dihydroxyacetone_kinase_(Dak1),_putative_54681..54831_POSITIVE 254 67 21 61 12 NC_009009:SSA_0425|3end_Glycosyltransferase,_putative_422230..422380_NEGATIVE 254 58 14 72 26 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 248 48 1 74 21 NC_009009:SSA_0587|3end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_579761..579911_POSITIVE 245 115 71 116 60 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 245 60 12 151 103 NC_009009:SSA_1081|3end_1-phosphofructokinase,_putative_1099269..1099419_POSITIVE 244 119 80 40 1 NC_009009:SSA_0942|3end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_950936..951086_POSITIVE 239 88 46 42 1 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 239 67 30 100 64 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 231 109 62 146 109 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 230 68 34 127 91 NC_009009:SSA_0419|3end_Alpha-galactosidase,_putative_418530..418680_POSITIVE 229 80 33 87 34 NC_009009:SSA_0791|3end_UDP-N-acetylglucosamine-like_protein,_putative_774705..774855_POSITIVE 229 50 1 58 2 NC_009009:SSA_0215|3end_Periplasmic_sugar-binding_protein_(ribose_porter),_putative_211957..212107_POSITIVE 227 57 17 47 10 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 227 68 25 88 48 NC_009009:SSA_1504|3end_hypothetical_protein_1506459..1506609_NEGATIVE 224 97 54 77 21 NC_009009:SSA_0291|3end_Oxidoreductase,_putative_286269..286419_POSITIVE 224 57 14 96 46 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE