Origin IGS: tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcttatcttctccattcatcttttcaatccaaaccattataccataaatccttatcctaaacagcggatttaagttattttttctagctttctttacaaaaatgtaaaataaattgaagaaaaaaatggtataatatagctaatattcttattaaaggagtcccta Mask Tandem Repeat Region ================================================ tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga Find is-nt database================================================ Query_seq: SSA_0004:SSA_0005|SSA_0004:SSA_0005:Lipoprotein, putative:GTP-binding protein, putative:<-->:3795..3960 166 tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0004:SSA_0005|SSA_0004:SSA_0005:Lipoprotein, putative:GTP-binding protein, putative:<-->:3795..3960 166 tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0004:SSA_0005|SSA_0004:SSA_0005:Lipoprotein, putative:GTP-binding protein, putative:<-->:3795..3960 166 tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 40 End: 165 ....................................... M F F F N L F Y I F V K K A R K N N L N P L F R I R I Y G I M V W I E K M N G E D K . tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga 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================================================ tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0004:SSA_0005|SSA_0004:SSA_0005:Lipoprotein, putative:GTP-binding protein, putative:<-->:3795..3960 166 tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_009009_SSA_0004_SSA_0005|Lipoprotein, putative:GTP-binding protein, putative|NEGATIVE:POSITIVE|[3795,3960]|166 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 tagggactcctttaataagaatattagctatattataccannnnnnncttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga tagggactcctttaataagaatattagctatattataccatttttttcttcaatttattttacatttttgtaaagaaagctagaaaaaataacttaaatccgctgtttaggataaggatttatggtataatggtttggattgaaaagatgaatggagaagataaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGGACUCCUUUAAUAAGAAUAUUAGCUAUAUUAUACCAUUUUUUUCUUCAAUUUAUUUUACAUUUUUGUAAAGAAAGCUAGAAAAAAUAACUUAAAUCCGCUGUUUAGGAUAAGGAUUUAUGGUAUAAUGGUUUGGAUUGAAAAGAUGAAUGGAGAAGAUAAGA ......((((((((........(((.....(((((((((..((((((((....(((.(((((((....))))))))))...)))))))).....(((((((.((.....))....))))))).))))))))).....)))........)))).))))......... (-33.39) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUAUCUUCUCCAUUCAUCUUUUCAAUCCAAACCAUUAUACCAUAAAUCCUUAUCCUAAACAGCGGAUUUAAGUUAUUUUUUCUAGCUUUCUUUACAAAAAUGUAAAAUAAAUUGAAGAAAAAAAUGGUAUAAUAUAGCUAAUAUUCUUAUUAAAGGAGUCCCUA .........((((......................((((((((((((((((..............))))))).....(((((((........((((((....)))))).......)))))))....))))))))).....(((((....)))))..))))...... (-26.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 791 140 91 231 182 NC_009009:SSA_0004|5end_Lipoprotein,_putative_3704..3934_NEGATIVE 293 158 113 167 123 NC_009009:SSA_0846|5end_DNA-polymerase_III_alpha-chain,_putative_830078..830308_POSITIVE 270 49 3 146 92 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 267 158 131 135 107 NC_009009:SSA_1862|5end_hypothetical_protein_1858541..1858771_NEGATIVE 261 137 100 75 39 NC_009009:SSA_0282|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIA_component,_putative_274215..274445_POSITIVE 239 80 33 120 73 NC_009009:SSA_0945|5end_Phosphate_import_ATP-binding_protein_pstB_1,_putative_952605..952835_POSITIVE 236 138 98 196 155 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 235 40 1 129 91 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 235 135 92 45 1 NC_009009:SSA_0136|5end_ABC_transporter,_Zn_porter,_putative_131014..131244_POSITIVE 229 138 100 230 185 NC_009009:SSA_1993|5end_Conserved_uncharacterized_protein_1990790..1991020_NEGATIVE 224 142 101 231 183 NC_009009:SSA_1962|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960110..1960340_POSITIVE 222 160 115 226 171 NC_009009:SSA_0236|5end_Chromosome_segregation_helicase,_putative_232443..232673_NEGATIVE 216 133 97 222 181 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 214 140 98 226 181 NC_009009:SSA_2193|5end_ADP-ribose_pyrophosphatase,_putative_2194793..2195023_NEGATIVE 213 40 6 135 103 NC_009009:SSA_0019|5end_Secreted_antigen_GbpB/SagA;_peptidoglycan_hydrolase;_PcsB_protein_precursor,_putative_24225..24455_POSITIVE 211 150 102 165 115 NC_009009:SSA_2303|5end_hypothetical_protein_2305177..2305407_NEGATIVE 211 150 106 199 143 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 208 149 102 62 19 NC_009009:SSA_0669|5end_ATP_dependent_protease,_putative_653720..653950_NEGATIVE 207 45 8 137 103 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 207 146 117 211 180 NC_009009:SSA_0865|5end_hypothetical_protein_856378..856608_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 158 131 87 59 NC_009009:SSA_1863|3end_NH(3)-dependent_NAD(+)_synthetase,_putative_1858589..1858739_NEGATIVE 244 135 91 48 3 NC_009009:SSA_0135|3end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_131097..131247_POSITIVE 239 80 33 59 12 NC_009009:SSA_0944|3end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_952624..952774_POSITIVE 238 140 92 79 37 NC_009009:SSA_1753|3end_Transcriptional_regulator,_GntR_family_(repressor_of_trehalose_operon),_putative_1742740..1742890_POSITIVE 235 40 1 58 20 NC_009009:SSA_1920|3end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1910884..1911034_POSITIVE 225 51 17 120 84 NC_009009:SSA_2265|3end_Maltodextrin_phosphorylase,_putative_2261936..2262086_NEGATIVE 221 147 102 53 8 NC_009009:SSA_1773|3end_hypothetical_protein_1759535..1759685_NEGATIVE 213 40 6 38 6 NC_009009:SSA_0018|3end_Cell-shape_determining_protein_MreD,_putative_24208..24358_POSITIVE 203 135 96 48 5 NC_009009:SSA_1440|3end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444407..1444557_NEGATIVE 203 43 2 75 29 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 200 80 33 109 62 NC_009009:SSA_2333|3end_Integral_membrane_protein,_putative_2335216..2335366_NEGATIVE 200 160 117 69 34 NC_009009:SSA_1832|3end_hypothetical_protein_1822614..1822764_POSITIVE 200 106 65 135 102 NC_009009:SSA_0530|3end_Ethanolamine_utilization_protein_(transporter),_putative_527417..527567_POSITIVE 198 137 109 108 80 NC_009009:SSA_0330|3end_hypothetical_protein_325162..325312_POSITIVE 192 150 103 74 5 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 192 117 78 68 42 NC_009009:SSA_1685|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1678390..1678540_NEGATIVE 192 144 108 145 113 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 191 146 102 148 107 NC_009009:SSA_2304|3end_Conserved_uncharacterized_protein_2305185..2305335_NEGATIVE 191 49 9 48 1 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 189 142 101 108 70 NC_009009:SSA_1783|3end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1768102..1768252_NEGATIVE