Origin IGS: tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 cactgctagccatttttgtttaactttaagatttttcaaggtagtatctccttttcttatttatcatgctttattatagcctagttgcatatcggtttcgctgtatcataaagagaaatgaagattttcccaaaagatttatctgattctcttttcgaaaatacaagctcatgcaaagcaaaatagatttttagcttcaattcaatccgaagcaacgcacctcttattaatcggccaatcaaaagatcaaagtctgcttgggataactga Mask Tandem Repeat Region ================================================ tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg Find is-nt database================================================ Query_seq: SSA_0156:SSA_0157|SSA_0156:SSA_0157:ATPase with chaperone activity, ATP-binding subunit, putative:hypothetical protein:->->:153383..153652 270 tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0156:SSA_0157|SSA_0156:SSA_0157:ATPase with chaperone activity, ATP-binding subunit, putative:hypothetical protein:->->:153383..153652 270 tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0156:SSA_0157|SSA_0156:SSA_0157:ATPase with chaperone activity, ATP-binding subunit, putative:hypothetical protein:->->:153383..153652 270 tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 29 End: 187 ............................ M I G R L I R G A L L R I E L K L K I Y F A L H E L V F S K R E S D K S F G K I F I S L Y D T A K P I C N ................................................................................... Protein_Len: 36 Strand: + Start: 87 End: 194 ...................................................................................... M L L C M S L Y F R K E N Q I N L L G K S S F L F M I Q R N R Y A T R L ............................................................................ Protein_Len: 44 Strand: - Start: 3 End: 134 .. T I G L L S Q D K S Q G I L L L H T A E S Q I S A L F R N Q K A H A Q I K S F L I L Y M ........................................................................................................................................ tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg 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: 137 End: 166 ........................................................................................................................................TTTGGGAAAATCTTCATTTCTCTTTATGAT........................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0156:SSA_0157|SSA_0156:SSA_0157:ATPase with chaperone activity, ATP-binding subunit, putative:hypothetical protein:->->:153383..153652 270 tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg Intra-Species Hit: Count: 1 Min: 1 Max: 270 Len: 270 Subject: NC_009009_SSA_0156_SSA_0157|ATPase with chaperone activity, ATP-binding subunit, putative:hypothetical protein|POSITIVE:POSITIVE|[153383,153652]|270 HSP 1 e-value: 1.0E-151 bit: 535.0 Len: 270 Query Start:1 Query End:270 Subject Strand: POSITIVE Subject Start: 1 Subject End: 270 tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg tcagttatcccaagcagactttgatcttttgattggccgattaataagaggtgcgttgcttcggattgaattgaagctaaaaatctattttgctttgcatgagcttgtattttcgaaaagagaatcagataaatcttttgggaaaatcttcatttctctttatgatacagcgaaaccgatatgcaactaggctataataaagcatgataaataagaaaaggagatactaccttgaaaaatcttaaagttaaacaaaaatggctagcagtg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAGUUAUCCCAAGCAGACUUUGAUCUUUUGAUUGGCCGAUUAAUAAGAGGUGCGUUGCUUCGGAUUGAAUUGAAGCUAAAAAUCUAUUUUGCUUUGCAUGAGCUUGUAUUUUCGAAAAGAGAAUCAGAUAAAUCUUUUGGGAAAAUCUUCAUUUCUCUUUAUGAUACAGCGAAACCGAUAUGCAACUAGGCUAUAAUAAAGCAUGAUAAAUAAGAAAAGGAGAUACUACCUUGAAAAAUCUUAAAGUUAAACAAAAAUGGCUAGCAGUG ((((((((((.((((((.......((((((((((....)))))).))))......)))))).))))..)))))).((((......((((.(((((((....((((((.....(((.((((((((..((((...(((....)))..))))....)))))))).)))..((.((....))...))....))))))....))))))).))))..(((((.((((........))))......)))))..................)))).... (-55.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACUGCUAGCCAUUUUUGUUUAACUUUAAGAUUUUUCAAGGUAGUAUCUCCUUUUCUUAUUUAUCAUGCUUUAUUAUAGCCUAGUUGCAUAUCGGUUUCGCUGUAUCAUAAAGAGAAAUGAAGAUUUUCCCAAAAGAUUUAUCUGAUUCUCUUUUCGAAAAUACAAGCUCAUGCAAAGCAAAAUAGAUUUUUAGCUUCAAUUCAAUCCGAAGCAACGCACCUCUUAUUAAUCGGCCAAUCAAAAGAUCAAAGUCUGCUUGGGAUAACUGA ....(((((.....(((((((.....(((((......((((........)))).))))).......((((((.....((((............))))..((((((((..((((((((....((((..((......))...))))..))))))))..))...))).)))......)))))))))))))...))))).........((((.(((((((.....((((.................)))).....)).))))).))))...... (-44.13) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 68 25 62 21 NC_009009:SSA_0370|5end_Acetyltransferase,_GNAT_family,_putative_360382..360612_NEGATIVE 289 78 32 78 30 NC_009009:SSA_0736|5end_Catabolite_gene_activator_and_regulatory_subunit_of_cAMP-dependent_protein_kinases,_putative_717648..717878_POSITIVE 282 60 12 209 164 NC_009009:SSA_0397|5end_hypothetical_protein_394657..394887_NEGATIVE 278 78 33 152 92 NC_009009:SSA_1247|5end_hypothetical_protein_1272358..1272588_NEGATIVE 270 86 46 75 37 NC_009009:SSA_0615|5end_RggD,_putative_609195..609425_NEGATIVE 264 60 11 78 40 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 261 60 13 230 183 NC_009009:SSA_1629|5end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1630338..1630568_POSITIVE 259 57 13 54 3 NC_009009:SSA_1731|5end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716808..1717038_NEGATIVE 259 192 156 61 33 NC_009009:SSA_1084|5end_Conserved_uncharacterized_protein_1101675..1101905_POSITIVE 258 41 1 74 18 NC_009009:SSA_2200|5end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201573..2201803_NEGATIVE 258 78 36 168 130 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 257 98 51 150 94 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 255 69 24 148 105 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 254 167 125 64 24 NC_009009:SSA_1710|5end_Transcriptional_regulator,_XRE_family,_putative_1698338..1698568_POSITIVE 254 183 148 140 95 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 253 60 13 94 57 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 252 193 153 194 151 NC_009009:SSA_0536|5end_B12-dependent_diol_dehydratase_small_subunit,_putative_531342..531572_POSITIVE 252 60 11 201 147 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 247 80 31 76 28 NC_009009:SSA_1497|5end_DCMP_deaminase,_putative_1503535..1503765_NEGATIVE 247 65 33 59 32 NC_009009:SSA_0988|5end_TfoX_N-terminal_domain_family_protein,_putative_990662..990892_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 49 1 66 17 NC_009009:SSA_0156|3end_ATPase_with_chaperone_activity,_ATP-binding_subunit,_putative_153322..153472_POSITIVE 278 77 32 72 28 NC_009009:SSA_1062|3end_50S_ribosomal_protein_L27,_putative_1078657..1078807_POSITIVE 269 72 37 87 56 NC_009009:SSA_0771|3end_Glutaredoxin-like_protein,_putative_751572..751722_NEGATIVE 267 54 13 45 4 NC_009009:SSA_1750|3end_Extracellular_nuclease,_putative_1735673..1735823_NEGATIVE 264 60 11 74 36 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 259 192 156 58 30 NC_009009:SSA_1083|3end_Conserved_uncharacterized_protein_1101752..1101902_POSITIVE 257 98 51 140 84 NC_009009:SSA_0238|3end_hypothetical_protein_233031..233181_POSITIVE 255 69 24 136 93 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 253 60 13 97 60 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 252 60 11 106 52 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 250 60 19 133 84 NC_009009:SSA_1428|3end_hypothetical_protein_1435638..1435788_NEGATIVE 248 68 35 31 1 NC_009009:SSA_0371|3end_NADP-specific_glutamate_dehydrogenase,_putative_360413..360563_NEGATIVE 246 159 123 78 38 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 246 40 1 141 99 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 242 190 146 59 8 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 240 70 21 145 85 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 239 42 2 118 88 NC_009009:SSA_1972|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1967811..1967961_NEGATIVE 238 100 56 101 52 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 236 78 31 59 3 NC_009009:SSA_0639|3end_hypothetical_protein_627733..627883_NEGATIVE 236 195 151 94 62 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE