Origin IGS: gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta .........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 taggaaatctcctttgtgtaaaacattctatatttagtataacaaatatcgaaagcgctttcaaacaaaaaatagaaaaacatacaaagatgttcaaaatagtttctcaggtgaattgctgagcatatgagaatcttccttgtttcaagtgctatttgtaatatccgaaccttctgcctttattttctgaaatagtatacaaaatcctcgaatttatgctacaatgagacaaactaaaaatgattggagccaagc Mask Tandem Repeat Region ================================================ gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta Find is-nt database================================================ Query_seq: SSA_2019:SSA_2020|SSA_2019:SSA_2020:hypothetical protein:hypothetical protein:<-->:2019169..2019423 255 gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2019:SSA_2020|SSA_2019:SSA_2020:hypothetical protein:hypothetical protein:<-->:2019169..2019423 255 gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2019:SSA_2020|SSA_2019:SSA_2020:hypothetical protein:hypothetical protein:<-->:2019169..2019423 255 gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 3 End: 101 .. M A P I I F S L S H C S I N S R I L Y T I S E N K G R R F G Y Y K .......................................................................................................................................................... Protein_Len: 54 Strand: + Start: 92 End: 253 ........................................................................................... M L Q I A L E T R K I L I C S A I H L R N Y F E H L C M F F Y F L F E S A F D I C Y T K Y R M F Y T K E I S .. Protein_Len: 33 Strand: + Start: 156 End: 254 ........................................................................................................................................................... M L N I F V C F S I F C L K A L S I F V I L N I E C F T Q R R F P . Protein_Len: 30 Strand: - Start: 137 End: 226 ........................................................................................................................................ C N V Q S V I K F M K T H K E I K Q K F A S E I N T I S F M ............................. gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta 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: 191 End: 220 ..............................................................................................................................................................................................TTTGAAAGCGCTTTCGATATTTGTTATACT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2019:SSA_2020|SSA_2019:SSA_2020:hypothetical protein:hypothetical protein:<-->:2019169..2019423 255 gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta Intra-Species Hit: Count: 1 Min: 1 Max: 255 Len: 255 Subject: NC_009009_SSA_2019_SSA_2020|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2019169,2019423]|255 HSP 1 e-value: 1.0E-142 bit: 505.0 Len: 255 Query Start:1 Query End:255 Subject Strand: POSITIVE Subject Start: 1 Subject End: 255 gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta gcttggctccaatcatttttagtttgtctcattgtagcataaattcgaggattttgtatactatttcagaaaataaaggcagaaggttcggatattacaaatagcacttgaaacaaggaagattctcatatgctcagcaattcacctgagaaactattttgaacatctttgtatgtttttctattttttgtttgaaagcgctttcgatatttgttatactaaatatagaatgttttacacaaaggagatttccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUGGCUCCAAUCAUUUUUAGUUUGUCUCAUUGUAGCAUAAAUUCGAGGAUUUUGUAUACUAUUUCAGAAAAUAAAGGCAGAAGGUUCGGAUAUUACAAAUAGCACUUGAAACAAGGAAGAUUCUCAUAUGCUCAGCAAUUCACCUGAGAAACUAUUUUGAACAUCUUUGUAUGUUUUUCUAUUUUUUGUUUGAAAGCGCUUUCGAUAUUUGUUAUACUAAAUAUAGAAUGUUUUACACAAAGGAGAUUUCCUA ......((((..(((....((((((.((..(((((((((((.(((((((..((((((....(((((....)))))...))))))..))))))).............((((...))))...........))))))..)))))......)).))))))...))).......((((.....((((((.(((.((((((((....))))))..........)).))).)))))).....))))....))))........ (-45.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAAAUCUCCUUUGUGUAAAACAUUCUAUAUUUAGUAUAACAAAUAUCGAAAGCGCUUUCAAACAAAAAAUAGAAAAACAUACAAAGAUGUUCAAAAUAGUUUCUCAGGUGAAUUGCUGAGCAUAUGAGAAUCUUCCUUGUUUCAAGUGCUAUUUGUAAUAUCCGAACCUUCUGCCUUUAUUUUCUGAAAUAGUAUACAAAAUCCUCGAAUUUAUGCUACAAUGAGACAAACUAAAAAUGAUUGGAGCCAAGC ..((.((((..((((((((......((((((.....((((.....)))).((((....)))).........))))))....))))))))..........((((((((((((...(((((..(((((.(((((..........))))).)))))....)))))..))..........................(((((((...............)))))))...)))))..))))).....))))....)).... (-39.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 846 50 1 141 92 NC_009009:SSA_2019|5end_hypothetical_protein_2019078..2019308_NEGATIVE 293 42 7 133 98 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 290 179 133 105 60 NC_009009:SSA_1431|5end_hypothetical_protein_1438730..1438960_NEGATIVE 282 148 104 60 18 NC_009009:SSA_2364|5end_Immunodominant_staphylococcal_antigen_A_precursor,_putative_2367032..2367262_NEGATIVE 281 70 24 186 138 NC_009009:SSA_1596|5end_hypothetical_protein_1603034..1603264_NEGATIVE 276 208 164 139 100 NC_009009:SSA_1081|5end_1-phosphofructokinase,_putative_1098278..1098508_POSITIVE 275 49 3 136 81 NC_009009:SSA_0899|5end_Conserved_permease,_putative_889903..890133_POSITIVE 271 49 5 176 129 NC_009009:SSA_1477|5end_Truncated_transposase,_putative_1482496..1482726_POSITIVE 271 49 5 175 128 NC_009009:SSA_0732|5end_Transposase,_putative_715896..716126_NEGATIVE 259 151 113 169 123 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 258 148 103 64 18 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 250 155 117 200 150 NC_009009:SSA_1003|5end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1003875..1004105_POSITIVE 249 43 1 135 93 NC_009009:SSA_0356|5end_Dipeptidase,_putative_349259..349489_POSITIVE 247 149 103 208 158 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 247 149 101 82 24 NC_009009:SSA_0856|5end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_843210..843440_POSITIVE 244 47 6 137 76 NC_009009:SSA_0736|5end_Catabolite_gene_activator_and_regulatory_subunit_of_cAMP-dependent_protein_kinases,_putative_717648..717878_POSITIVE 243 214 177 160 120 NC_009009:SSA_0148|5end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_142257..142487_POSITIVE 242 43 1 62 20 NC_009009:SSA_1853|5end_S-ribosylhomocysteine_lyase,_putative_1848642..1848872_POSITIVE 240 49 1 141 94 NC_009009:SSA_1982|5end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975873..1976103_NEGATIVE 240 46 1 96 61 NC_009009:SSA_1865|5end_Thioredoxin_reductase,_putative_1861892..1862122_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 208 164 142 103 NC_009009:SSA_1080|3end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1098361..1098511_POSITIVE 271 49 5 48 1 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 254 215 174 143 98 NC_009009:SSA_1399|3end_hypothetical_protein_1411659..1411809_NEGATIVE 249 43 1 56 14 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 244 47 6 89 28 NC_009009:SSA_0735|3end_Integral_membrane_protein,_putative_717680..717830_POSITIVE 243 164 131 36 4 NC_009009:SSA_0729|3end_hypothetical_protein_714677..714827_POSITIVE 238 38 1 133 95 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 237 150 114 89 63 NC_009009:SSA_0730|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_715167..715317_POSITIVE 233 206 163 117 72 NC_009009:SSA_2022|3end_Transcriptional_regulator,_MerR_family_(multidrug-efflux_transporter_genes),_putative_2024488..2024638_POSITIVE 230 148 106 58 22 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 229 190 141 126 63 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 229 129 81 94 43 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 226 208 174 123 84 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 226 39 7 56 19 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 224 140 99 56 18 NC_009009:SSA_0903|3end_NAD(P)H_dehydrogenase_(quinone),_putative_893813..893963_POSITIVE 222 50 2 95 53 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 220 230 184 109 50 NC_009009:SSA_1136|3end_ATPases_with_chaperone_activity,_ATP-binding_subunit,_putative_1164247..1164397_POSITIVE 220 172 131 110 69 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 219 125 81 64 11 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 218 140 103 45 1 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE