Origin IGS: taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg .........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 cctgctgtttaaagtgtttttagagaatagtataagttaaacttgtctattttttgcttggtcaaagaaaatatttggcaaaaaagctgtaaaagtctgtttttaacgtctaaactaaatgttattgtaatgtttgacttgttaatgtaactttttggtaatattttatgtgtaagatagtattatcaccgaaaggagaattacatttta Mask Tandem Repeat Region ================================================ taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg Find is-nt database================================================ Query_seq: SSA_2364:SSA_2365|SSA_2364:SSA_2365:Immunodominant staphylococcal antigen A precursor, putative:Cobalt transport protein cbiQ, putative:<-<-:2367123..2367332 210 taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2364:SSA_2365|SSA_2364:SSA_2365:Immunodominant staphylococcal antigen A precursor, putative:Cobalt transport protein cbiQ, putative:<-<-:2367123..2367332 210 taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2364:SSA_2365|SSA_2364:SSA_2365:Immunodominant staphylococcal antigen A precursor, putative:Cobalt transport protein cbiQ, putative:<-<-:2367123..2367332 210 taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 47 End: 199 .............................................. M L P K S Y I N K S N I T I T F S L D V K N R L L Q L F C Q I F S L T K Q K I D K F N L Y Y S L K T L ........... Protein_Len: 35 Strand: - Start: 64 End: 168 ............................................................... M L L D F M V I V N L K S T L F L S K C S K Q W I N E K V L C F I S M .......................................... taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg 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================================================ taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2364:SSA_2365|SSA_2364:SSA_2365:Immunodominant staphylococcal antigen A precursor, putative:Cobalt transport protein cbiQ, putative:<-<-:2367123..2367332 210 taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg Intra-Species Hit: Count: 1 Min: 1 Max: 210 Len: 210 Subject: NC_009009_SSA_2364_SSA_2365|Immunodominant staphylococcal antigen A precursor, putative:Cobalt transport protein cbiQ, putative|NEGATIVE:NEGATIVE|[2367123,2367332]|210 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 210 Query Start:1 Query End:210 Subject Strand: POSITIVE Subject Start: 1 Subject End: 210 taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg taaaatgtaattctcctttcggtgataatactatcttacacataaaatattaccaaaaagttacattaacaagtcaaacattacaataacatttagtttagacgttaaaaacagacttttacagcttttttgccaaatattttctttgaccaagcaaaaaatagacaagtttaacttatactattctctaaaaacactttaaacagcagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUGUAAUUCUCCUUUCGGUGAUAAUACUAUCUUACACAUAAAAUAUUACCAAAAAGUUACAUUAACAAGUCAAACAUUACAAUAACAUUUAGUUUAGACGUUAAAAACAGACUUUUACAGCUUUUUUGCCAAAUAUUUUCUUUGACCAAGCAAAAAAUAGACAAGUUUAACUUAUACUAUUCUCUAAAAACACUUUAAACAGCAGG ...(((((((((....(((.(((((((....................))))))).))))))))))))...((((.((((...............((((((((.(((.......))).)))).))))(((((((((((.......)))).....)))))))........)))).))))................................. (-21.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUGCUGUUUAAAGUGUUUUUAGAGAAUAGUAUAAGUUAAACUUGUCUAUUUUUUGCUUGGUCAAAGAAAAUAUUUGGCAAAAAAGCUGUAAAAGUCUGUUUUUAACGUCUAAACUAAAUGUUAUUGUAAUGUUUGACUUGUUAAUGUAACUUUUUGGUAAUAUUUUAUGUGUAAGAUAGUAUUAUCACCGAAAGGAGAAUUACAUUUUA ..((((((((((((((((.((((((((((..(((((((((((......((((((.((((.((((((.......))))))....))))...)))))).......((((((.........)))))).......)))))))))))...)))...))))))).))))))))).......)))))))...((.((....)).))........... (-39.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 736 60 11 151 102 NC_009009:SSA_2364|5end_Immunodominant_staphylococcal_antigen_A_precursor,_putative_2367032..2367262_NEGATIVE 283 155 112 114 65 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 241 130 90 142 98 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 233 150 112 187 144 NC_009009:SSA_1320|5end_hypothetical_protein_1337194..1337424_NEGATIVE 227 156 112 219 168 NC_009009:SSA_0010|5end_Cell_division_protein_DivIC,_putative_9424..9654_POSITIVE 225 156 111 95 45 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 225 166 122 68 29 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 223 154 112 230 185 NC_009009:SSA_1339|5end_Pneumococcal_histidine_triad_protein_D_precursor,_putative_1355424..1355654_NEGATIVE 220 201 174 113 86 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 219 168 124 125 77 NC_009009:SSA_2296|5end_Transcriptional_regulator,_XRE_family,_putative_2298773..2299003_NEGATIVE 217 43 13 30 1 NC_009009:SSA_0634|5end_Anthranilate_phosphoribosyltransferase,_putative_623387..623617_POSITIVE 213 156 112 53 12 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 213 135 103 62 31 NC_009009:SSA_0108|5end_50S_ribosomal_protein_L4,_putative_108816..109046_POSITIVE 210 155 117 53 11 NC_009009:SSA_2198|5end_hypothetical_protein_2198585..2198815_NEGATIVE 210 155 113 118 72 NC_009009:SSA_1449|5end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1451931..1452161_NEGATIVE 210 160 111 231 178 NC_009009:SSA_0751|5end_Oligoendopeptidase_F,_putative_732367..732597_POSITIVE 209 136 95 226 179 NC_009009:SSA_2265|5end_Maltodextrin_phosphorylase,_putative_2264197..2264427_NEGATIVE 209 156 135 29 7 NC_009009:SSA_1999|5end_hypothetical_protein_1996974..1997204_NEGATIVE 209 155 112 173 140 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 209 155 112 159 120 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 135 96 88 40 NC_009009:SSA_0525|3end_Microcompartment_protein,_putative_523842..523992_POSITIVE 241 130 90 140 96 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 237 156 122 130 92 NC_009009:SSA_0303|3end_surface_protein_C_301051..301201_POSITIVE 233 150 112 135 92 NC_009009:SSA_1321|3end_Ferrochelatase,_putative_1337246..1337396_NEGATIVE 219 168 124 122 74 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 214 149 107 122 79 NC_009009:SSA_1643|3end_hypothetical_protein_1644610..1644760_NEGATIVE 213 135 103 37 6 NC_009009:SSA_0107|3end_50S_ribosomal_protein_L3,_putative_108871..109021_POSITIVE 211 136 102 65 28 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 211 155 116 137 97 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 209 155 112 117 84 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 207 151 115 151 121 NC_009009:SSA_0249|3end_hypothetical_protein_242115..242265_POSITIVE 203 165 123 44 6 NC_009009:SSA_0750|3end_hypothetical_protein_732255..732405_POSITIVE 201 155 123 53 22 NC_009009:SSA_1224|3end_hypothetical_protein_1247251..1247401_NEGATIVE 199 160 112 149 103 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 197 133 103 123 89 NC_009009:SSA_2329|3end_hypothetical_protein_2333169..2333319_POSITIVE 197 57 11 142 101 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 194 155 112 140 99 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 193 155 117 129 89 NC_009009:SSA_0796|3end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_779060..779210_POSITIVE 192 177 152 84 52 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 190 170 122 59 2 NC_009009:SSA_2177|3end_hypothetical_protein_2175232..2175382_NEGATIVE