Origin IGS: ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagatggattctccttttattttccgaggaaacccccgtttatctattctattttacaaaattttcgcctaaaaagctagcctatttcgtcaaatcagacctttttcaacaagaaagcgcttttgtatttccgagcagaaacctttgcc Mask Tandem Repeat Region ================================================ ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta Find is-nt database================================================ Query_seq: SSA_0687:SSA_0688|SSA_0687:SSA_0688:hypothetical protein:2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative:->->:671351..671499 149 ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0687:SSA_0688|SSA_0687:SSA_0688:hypothetical protein:2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative:->->:671351..671499 149 ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0687:SSA_0688|SSA_0687:SSA_0688:hypothetical protein:2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative:->->:671351..671499 149 ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: - Start: 2 End: 142 . C L N R S P F V F A S E Q Q F L D S K V F Y A L K K P S F K T F Y F L Y V P T E E S F L L L M ....... ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0687:SSA_0688|SSA_0687:SSA_0688:hypothetical protein:2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative:->->:671351..671499 149 ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: NC_009009_SSA_0687_SSA_0688|hypothetical protein:2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative|POSITIVE:POSITIVE|[671351,671499]|149 HSP 1 e-value: 2.0E-79 bit: 295.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta ggcaaaggtttctgctcggaaatacaaaagcgctttcttgttgaaaaaggtctgatttgacgaaataggctagctttttaggcgaaaattttgtaaaatagaatagataaacgggggtttcctcggaaaataaaaggagaatccatcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAAAGGUUUCUGCUCGGAAAUACAAAAGCGCUUUCUUGUUGAAAAAGGUCUGAUUUGACGAAAUAGGCUAGCUUUUUAGGCGAAAAUUUUGUAAAAUAGAAUAGAUAAACGGGGGUUUCCUCGGAAAAUAAAAGGAGAAUCCAUCUA ......((.((((.((......(((((((.(((((....(((......((((((.(((....)))))))))))).....)))))....)))))))................(((((....))))).........)).)))).))..... (-29.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUGGAUUCUCCUUUUAUUUUCCGAGGAAACCCCCGUUUAUCUAUUCUAUUUUACAAAAUUUUCGCCUAAAAAGCUAGCCUAUUUCGUCAAAUCAGACCUUUUUCAACAAGAAAGCGCUUUUGUAUUUCCGAGCAGAAACCUUUGCC (((((((....(((((.........))))).....)))))))..............((((..(((((((..(((.((.(((.......(((......)))..(((((.....))))).)))...)).)))..).)).))))..)))).. (-20.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 80 31 231 176 NC_009009:SSA_2035|5end_Conserved_uncharacterized_protein_2040288..2040518_NEGATIVE 296 76 31 179 133 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 290 84 47 51 9 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 281 75 33 227 184 NC_009009:SSA_0627|5end_hypothetical_protein_617314..617544_POSITIVE 279 60 12 58 6 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 278 50 1 208 151 NC_009009:SSA_1470|5end_3-dehydroquinate_dehydratase,_putative_1476984..1477214_NEGATIVE 276 57 12 50 13 NC_009009:SSA_1747|5end_hypothetical_protein_1733450..1733680_NEGATIVE 267 60 11 86 27 NC_009009:SSA_2131|5end_DNA-binding_protein,_putative_2133949..2134179_POSITIVE 263 50 6 148 92 NC_009009:SSA_0606|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_594532..594762_NEGATIVE 260 129 84 126 71 NC_009009:SSA_1959|5end_Undecaprenyl-diphosphatase,_putative_1956431..1956661_NEGATIVE 260 74 32 155 107 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 253 60 11 66 8 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 252 83 47 226 195 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 251 44 6 50 7 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 248 77 31 143 94 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 247 54 14 61 24 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 246 79 34 51 10 NC_009009:SSA_0595|5end_hypothetical_protein_586490..586720_POSITIVE 245 78 41 191 155 NC_009009:SSA_2178|5end_hypothetical_protein_2177595..2177825_NEGATIVE 244 35 1 200 169 NC_009009:SSA_2019|5end_hypothetical_protein_2019078..2019308_NEGATIVE 242 38 7 222 181 NC_009009:SSA_0403|5end_CAAX_amino_terminal_protease_family,_putative_400475..400705_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 75 33 45 2 NC_009009:SSA_0626|3end_hypothetical_protein_617212..617362_POSITIVE 267 60 11 77 18 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 263 50 6 90 34 NC_009009:SSA_0607|3end_ABC_transporter,_permease_component,_putative_594590..594740_NEGATIVE 253 60 11 127 69 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 252 71 32 148 104 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 251 84 48 72 37 NC_009009:SSA_2077|3end_hypothetical_protein_2081352..2081502_NEGATIVE 249 70 27 83 38 NC_009009:SSA_0067|3end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_69890..70040_POSITIVE 248 77 31 150 101 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 247 54 14 64 27 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 240 90 47 48 1 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 240 85 43 70 38 NC_009009:SSA_0208|3end_Conserved_uncharacterized_protein_204968..205118_NEGATIVE 232 75 35 150 119 NC_009009:SSA_1615|3end_Alanine_dehydrogenase,_putative_1619318..1619468_POSITIVE 231 59 11 49 1 NC_009009:SSA_1678|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1671336..1671486_NEGATIVE 231 60 12 65 27 NC_009009:SSA_0490|3end_Cobalamin_5'-phosphate_synthase,_putative_491044..491194_POSITIVE 227 87 49 103 68 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 225 85 48 88 44 NC_009009:SSA_1832|3end_hypothetical_protein_1822614..1822764_POSITIVE 225 44 6 90 37 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 223 77 31 98 66 NC_009009:SSA_0547|3end_Acyl_carrier_protein_synthase,_putative_542433..542583_POSITIVE 222 73 32 60 19 NC_009009:SSA_0274|3end_hypothetical_protein_268580..268730_NEGATIVE 221 59 11 151 96 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE