Origin IGS: aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gataagagactcctttcttttctttaatatgattatacaagacaaacttcaagaatttataaagtaattctaaaatatttctaaagaatgaaagaaattataaacataaacaaatcaaggattatcgccacttcaacttgtttgctatgcttcttatttttggactaaatgatgtcaaaaactctttaaagatctatctcaaaatctaagaaaagttgtagataaaaatgtggagattgaatttaaaaaaagaaaactgacaatgcgttaaaggaggaaaaaaagtcctaaaattttatcgcacaaagtcaaatttttagcctacctttcctagatgattttctttttagtcaaatacttccagctcctgctcatccacttcctccccctcgcggtctcaattttgcaggttcggtaacatgctaaaagctgttttttccttcttgccaacccgcttacattttgctaaaatgatgtcaaaaatcagtaaggaaaaatt Mask Tandem Repeat Region ================================================ aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc Find is-nt database================================================ Query_seq: SSA_0252:SSA_0253|SSA_0252:SSA_0253:hypothetical protein:CAAX amino terminal protease family protein, putative:<-->:245930..246428 499 aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0252:SSA_0253|SSA_0252:SSA_0253:hypothetical protein:CAAX amino terminal protease family protein, putative:<-->:245930..246428 499 aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0252:SSA_0253|SSA_0252:SSA_0253:hypothetical protein:CAAX amino terminal protease family protein, putative:<-->:245930..246428 499 aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 50 End: 166 ................................................. M A R R K K Q L L A C Y R T C K I E T A R G R K W M S R S W K Y L T K K K I I ............................................................................................................................................................................................................................................................................................................................................. Protein_Len: 44 Strand: - Start: 294 End: 425 ..................................................................................................................................................................................................................................................................................................... I K L Y I K L S N K V D N L G F I L L M A F L N F H R Y D K I Q K H K Y N R E N K L F M .......................................................................... Protein_Len: 42 Strand: - Start: 77 End: 202 ............................................................................ C T V S G A F N L G R P P P L P H A P A P L I Q S F L F D D L F P L S F I Q S Q A M ......................................................................................................................................................................................................................................................................................................... aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc 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: 88 Start: 28 End: 57 ...........................CTTGCCAACCCGCTTACATTTTGCTAAAAT.......................................................................................................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 424 End: 453 .......................................................................................................................................................................................................................................................................................................................................................................................................................................CTTCAAGAATTTATAAAGTAATTCTAAAAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0252:SSA_0253|SSA_0252:SSA_0253:hypothetical protein:CAAX amino terminal protease family protein, putative:<-->:245930..246428 499 aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc Intra-Species Hit: Count: 1 Min: 1 Max: 499 Len: 499 Subject: NC_009009_SSA_0252_SSA_0253|hypothetical protein:CAAX amino terminal protease family protein, putative|NEGATIVE:POSITIVE|[245930,246428]|499 HSP 1 e-value: 0.0 bit: 906.0 Len: 499 Query Start:1 Query End:499 Subject Strand: POSITIVE Subject Start: 1 Subject End: 499 aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggacnnnnnnncctcctttaacgcattgtcagttttcnnnnnnnaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc aatttttccttactgatttttgacatcattttagcaaaatgtaagcgggttggcaagaaggaaaaaacagcttttagcatgttaccgaacctgcaaaattgagaccgcgagggggaggaagtggatgagcaggagctggaagtatttgactaaaaagaaaatcatctaggaaaggtaggctaaaaatttgactttgtgcgataaaattttaggactttttttcctcctttaacgcattgtcagttttctttttttaaattcaatctccacatttttatctacaacttttcttagattttgagatagatctttaaagagtttttgacatcatttagtccaaaaataagaagcatagcaaacaagttgaagtggcgataatccttgatttgtttatgtttataatttctttcattctttagaaatattttagaattactttataaattcttgaagtttgtcttgtataatcatattaaagaaaagaaaggagtctcttatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUUCCUUACUGAUUUUUGACAUCAUUUUAGCAAAAUGUAAGCGGGUUGGCAAGAAGGAAAAAACAGCUUUUAGCAUGUUACCGAACCUGCAAAAUUGAGACCGCGAGGGGGAGGAAGUGGAUGAGCAGGAGCUGGAAGUAUUUGACUAAAAAGAAAAUCAUCUAGGAAAGGUAGGCUAAAAAUUUGACUUUGUGCGAUAAAAUUUUAGGACUUUUUUUCCUCCUUUAACGCAUUGUCAGUUUUCUUUUUUUAAAUUCAAUCUCCACAUUUUUAUCUACAACUUUUCUUAGAUUUUGAGAUAGAUCUUUAAAGAGUUUUUGACAUCAUUUAGUCCAAAAAUAAGAAGCAUAGCAAACAAGUUGAAGUGGCGAUAAUCCUUGAUUUGUUUAUGUUUAUAAUUUCUUUCAUUCUUUAGAAAUAUUUUAGAAUUACUUUAUAAAUUCUUGAAGUUUGUCUUGUAUAAUCAUAUUAAAGAAAAGAAAGGAGUCUCUUAUC .(((((((((...((((((((.......((((((((((......((......))...............(((((((((.((((.(((..(((.(..........((....)).).)))...)))...))))...))))))))).)))).)))))).))))))))...))))))))).(((((((...(((((...(((((.((((.....((((.......))))..)))).))))).)))))................((((.(((......(((((((.(((..((.....))..))))))))))........)))...)))).....))))))).....((((((.(((((...((((((((.(((.((......)))))))))))))))))).....(((((((((.((((((((...(((...(((...((((((........))))))...)))...)))......))))))))..))))))))).)))))). (-102.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAGAGACUCCUUUCUUUUCUUUAAUAUGAUUAUACAAGACAAACUUCAAGAAUUUAUAAAGUAAUUCUAAAAUAUUUCUAAAGAAUGAAAGAAAUUAUAAACAUAAACAAAUCAAGGAUUAUCGCCACUUCAACUUGUUUGCUAUGCUUCUUAUUUUUGGACUAAAUGAUGUCAAAAACUCUUUAAAGAUCUAUCUCAAAAUCUAAGAAAAGUUGUAGAUAAAAAUGUGGAGAUUGAAUUUAAAAAAAGAAAACUGACAAUGCGUUAAAGGAGGAAAAAAAGUCCUAAAAUUUUAUCGCACAAAGUCAAAUUUUUAGCCUACCUUUCCUAGAUGAUUUUCUUUUUAGUCAAAUACUUCCAGCUCCUGCUCAUCCACUUCCUCCCCCUCGCGGUCUCAAUUUUGCAGGUUCGGUAACAUGCUAAAAGCUGUUUUUUCCUUCUUGCCAACCCGCUUACAUUUUGCUAAAAUGAUGUCAAAAAUCAGUAAGGAAAAAUU ((.((((((....)))))).)).....((((.(((((..............((((((........))))))......((((........)))).....))))).)))).........(((...(((.((((......((((((((.((..((((((.((((((((........)))......(((....))).......)))))..))))))..)).))))))))....)))).))).............(((((..((((..((((.(((((.((((.......))))....))))).))))....))))..)))))..)))...((((((...((((((((.(((((((.((((......(((....)))...................((((..........(((((...((.((((.((.....))))))....))..)))))....))))....)))).))))))).))......))))))...)))))).... (-85.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1086 140 91 231 182 NC_009009:SSA_0252|5end_hypothetical_protein_245839..246069_NEGATIVE 361 138 91 190 151 NC_009009:SSA_1569|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571891..1572121_POSITIVE 359 142 109 74 28 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 347 147 103 84 23 NC_009009:SSA_1591|5end_Dipeptidase,_putative_1595451..1595681_NEGATIVE 340 130 86 197 149 NC_009009:SSA_0637|5end_Tryptophan_synthase_beta_chain,_putative_625719..625949_POSITIVE 340 130 89 168 126 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 339 145 104 203 157 NC_009009:SSA_0380|5end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_370916..371146_POSITIVE 334 136 91 50 4 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 333 140 92 54 2 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 332 150 102 161 96 NC_009009:SSA_2162|5end_hypothetical_protein_2160592..2160822_POSITIVE 332 139 91 171 123 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 331 144 102 51 1 NC_009009:SSA_0067|5end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_68005..68235_POSITIVE 324 130 83 74 25 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 318 140 92 62 10 NC_009009:SSA_1593|5end_Dipeptidase,_putative_1598054..1598284_NEGATIVE 314 144 101 60 8 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 314 150 103 231 190 NC_009009:SSA_0061|5end_Tagatose_1,6-diphosphate_aldolase,_putative_62670..62900_POSITIVE 313 120 90 56 18 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 313 140 91 224 175 NC_009009:SSA_0696|5end_hypothetical_protein_679154..679384_POSITIVE 312 131 91 160 120 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 311 140 92 212 159 NC_009009:SSA_0260|5end_Manganese/Zinc_ABC_transporter_substrate-binding_lipoprotein_precursor,_putative_254585..254815_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 142 109 64 18 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 338 140 100 57 8 NC_009009:SSA_0066|3end_hypothetical_protein_68095..68245_POSITIVE 334 136 91 48 2 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 333 140 92 61 9 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 332 139 91 150 102 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 317 140 99 149 101 NC_009009:SSA_0592|3end_hypothetical_protein_584248..584398_POSITIVE 312 131 91 47 7 NC_009009:SSA_0814|3end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_795519..795669_NEGATIVE 305 85 43 73 28 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 301 86 43 79 26 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 300 140 91 141 96 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 298 134 101 72 26 NC_009009:SSA_1325|3end_Ketoacyl_reductase_hetN,_putative_1341573..1341723_NEGATIVE 293 140 103 50 5 NC_009009:SSA_0261|3end_ABC-type_Mn2+/Zn2+_transport_systems,_permease_component,_putative_254605..254755_NEGATIVE 290 148 105 71 26 NC_009009:SSA_0461|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_464905..465055_POSITIVE 286 129 85 49 1 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 286 139 101 149 114 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 284 150 107 54 10 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 284 119 89 149 121 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 282 420 371 95 48 NC_009009:SSA_2019|3end_hypothetical_protein_2018812..2018962_NEGATIVE 279 140 98 73 13 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 279 150 104 85 42 NC_009009:SSA_0896|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_888441..888591_POSITIVE