Origin IGS: gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact .........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 agttacatttttgcttgacaatcctgctgtgaaattatagaatgaactaaatacaacctttaaagaagtccagagaggctactaaggtacatacgtttgaatggcagatactgccacattttcgtgtaaccttgctctcgggcaaggtttttctatgtctctgaacctagcgtgaaggtcaatttgaatataggagtgcctagcagagttctttaaagttaaaaattaaaaggagatttttccctc Mask Tandem Repeat Region ================================================ gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact Find is-nt database================================================ Query_seq: SSA_1241:SSA_1242|SSA_1241:SSA_1242:Orotidine-5'-phosphate decarboxylase, putative:Dihydroorotate dehydrogenase B, putative:<-<-:1266292..1266537 246 gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1241:SSA_1242|SSA_1241:SSA_1242:Orotidine-5'-phosphate decarboxylase, putative:Dihydroorotate dehydrogenase B, putative:<-<-:1266292..1266537 246 gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1241:SSA_1242|SSA_1241:SSA_1242:Orotidine-5'-phosphate decarboxylase, putative:Dihydroorotate dehydrogenase B, putative:<-<-:1266292..1266537 246 gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 58 End: 162 ......................................................... M Q I D L H A R F R D I E K P C P R A R L H E N V A V S A I Q T Y V P .................................................................................... Protein_Len: 32 Strand: + Start: 102 End: 197 ..................................................................................................... M P E S K V T R K C G S I C H S N V C T L V A S L D F F K G C I ................................................. Protein_Len: 37 Strand: - Start: 86 End: 196 ..................................................................................... L C L F V K G S L L T V R F H P L I Q W E F T H V K T A E R S K K L P Q M .................................................. gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact 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: 86 Start: 204 End: 233 ...........................................................................................................................................................................................................CTTGACAATCCTGCTGTGAAATTATAGAAT............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 89 HP_score: -7.7 Tail_Score: -5.08178 Start: 100 End: 117 Full_Region: cacattttcgtgtaa ccttgct ctcg ggcaagg tttttctatgtctct ...................................................................................................ccttgctctcgggcaagg................................................................................................................................. TransTerm Strand: - Conf: 73 HP_score: -10.0 Tail_Score: -2.51871 Start: 131 End: 145 Full_Region: gtacatacgtttgaa tggcag ata ctgcca cattttcgtgtaacc ..................................................................................................................................tggcagatactgcca..................................................................................................... Find igs database================================================ Query_seq: SSA_1241:SSA_1242|SSA_1241:SSA_1242:Orotidine-5'-phosphate decarboxylase, putative:Dihydroorotate dehydrogenase B, putative:<-<-:1266292..1266537 246 gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact Intra-Species Hit: Count: 1 Min: 1 Max: 246 Len: 246 Subject: NC_009009_SSA_1241_SSA_1242|Orotidine-5'-phosphate decarboxylase, putative:Dihydroorotate dehydrogenase B, putative|NEGATIVE:NEGATIVE|[1266292,1266537]|246 HSP 1 e-value: 1.0E-137 bit: 488.0 Len: 246 Query Start:1 Query End:246 Subject Strand: POSITIVE Subject Start: 1 Subject End: 246 gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact gagggaaaaatctccttttaatttttaactttaaagaactctgctaggcactcctatattcaaattgaccttcacgctaggttcagagacatagaaaaaccttgcccgagagcaaggttacacgaaaatgtggcagtatctgccattcaaacgtatgtaccttagtagcctctctggacttctttaaaggttgtatttagttcattctataatttcacagcaggattgtcaagcaaaaatgtaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGGAAAAAUCUCCUUUUAAUUUUUAACUUUAAAGAACUCUGCUAGGCACUCCUAUAUUCAAAUUGACCUUCACGCUAGGUUCAGAGACAUAGAAAAACCUUGCCCGAGAGCAAGGUUACACGAAAAUGUGGCAGUAUCUGCCAUUCAAACGUAUGUACCUUAGUAGCCUCUCUGGACUUCUUUAAAGGUUGUAUUUAGUUCAUUCUAUAAUUUCACAGCAGGAUUGUCAAGCAAAAAUGUAACU ((((((......))))))...((((((....))))))....((((.((((.((((...........((((((......(((((((((((........((((((((......))))))))..(((.....(((((((...))))))).....)))................))))))))))).....)))))).....(((......)))............)))).)))).))))........... (-61.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUACAUUUUUGCUUGACAAUCCUGCUGUGAAAUUAUAGAAUGAACUAAAUACAACCUUUAAAGAAGUCCAGAGAGGCUACUAAGGUACAUACGUUUGAAUGGCAGAUACUGCCACAUUUUCGUGUAACCUUGCUCUCGGGCAAGGUUUUUCUAUGUCUCUGAACCUAGCGUGAAGGUCAAUUUGAAUAUAGGAGUGCCUAGCAGAGUUCUUUAAAGUUAAAAAUUAAAAGGAGAUUUUUCCCUC ((((.((((((...((.(((.......))).)).....)))))))))).........((((((((((.((..(((((.....((((((..(((((......((((((...))))))......))))).)))))))))))..((.((((.((((((((((..(((.(((.......))))))....).))))))))).)))).)).)).))))))))))............(((.((....))))). (-64.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 948 120 71 211 162 NC_009009:SSA_1241|5end_Orotidine-5'-phosphate_decarboxylase,_putative_1266201..1266431_NEGATIVE 367 190 141 211 160 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 358 150 104 149 111 NC_009009:SSA_1364|5end_hypothetical_protein_1381297..1381527_NEGATIVE 326 120 71 156 103 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 326 46 1 72 22 NC_009009:SSA_1562|5end_hypothetical_protein_1566364..1566594_NEGATIVE 325 145 104 49 7 NC_009009:SSA_1971|5end_hypothetical_protein_1967167..1967397_POSITIVE 324 120 71 175 126 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 313 87 41 216 170 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 311 110 64 68 13 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 306 79 35 48 3 NC_009009:SSA_1559|5end_Conserved_uncharacterized_protein_1561656..1561886_NEGATIVE 296 140 98 46 1 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 296 178 131 112 76 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 295 118 71 146 100 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 291 150 101 67 7 NC_009009:SSA_1786|5end_Conserved_uncharacterized_protein_1770244..1770474_NEGATIVE 291 109 64 67 21 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 291 148 107 211 176 NC_009009:SSA_0811|5end_hypothetical_protein_792469..792699_POSITIVE 290 117 73 186 140 NC_009009:SSA_1224|5end_hypothetical_protein_1247481..1247711_NEGATIVE 289 90 41 189 128 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 288 178 131 108 61 NC_009009:SSA_1194|5end_Aspartate-semialdehyde_dehydrogenase,_putative_1221189..1221419_NEGATIVE 288 126 89 171 124 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 150 104 94 56 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE 306 79 35 46 1 NC_009009:SSA_1560|3end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1561658..1561808_NEGATIVE 304 114 79 62 24 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 296 178 131 112 76 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 295 118 71 141 95 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 290 117 73 78 32 NC_009009:SSA_1225|3end_Branched-chain_amino_acid_aminotransferase,_putative_1247589..1247739_NEGATIVE 289 110 69 72 32 NC_009009:SSA_1357|3end_hypothetical_protein_1372077..1372227_NEGATIVE 288 126 89 86 39 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 287 170 128 146 97 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 282 120 76 59 8 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 280 145 101 53 2 NC_009009:SSA_1727|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1712467..1712617_NEGATIVE 279 204 161 83 47 NC_009009:SSA_1703|3end_Methionyl-tRNA_synthetase,_putative_1693640..1693790_NEGATIVE 278 146 101 89 45 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 277 116 76 81 33 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 275 146 101 65 24 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 273 145 105 55 2 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 273 208 166 128 92 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 272 55 19 137 94 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 271 88 41 65 16 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 271 178 131 148 97 NC_009009:SSA_1736|3end_L-cysteine_desulfhydrase,_putative_1721453..1721603_NEGATIVE