Origin IGS: gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt .........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 aatgtgacctccttattaatttattttattataccacttatttgcattaaatgacacttcgttctgtatatgatacaatattaatgaatcagacaatgaatattcaggctatgcaaccgaaaatgatgcgatttcataaataacaaaatagtgcatttatccatcactccctaaataatcacagtcatctttttaaaaagcgagatcctttacacatttttaaaaagttattctcatcaaaaatttcattgctttaaggactcttttttactcattaggatgagtcagccctatgaaagccatagatactaaatccaaaatatgtttgttataaaatacttcgttttgtttaaggtgttatttttgtcatttaaaacttgtattctggttac Mask Tandem Repeat Region ================================================ gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt Find is-nt database================================================ Query_seq: SSA_0296:SSA_0297|SSA_0296:SSA_0297:Transcriptional regulator, XRE family, putative:Malolactic enzyme, putative:<-->:289454..289845 392 gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0296:SSA_0297|SSA_0296:SSA_0297:Transcriptional regulator, XRE family, putative:Malolactic enzyme, putative:<-->:289454..289845 392 gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0296:SSA_0297|SSA_0296:SSA_0297:Transcriptional regulator, XRE family, putative:Malolactic enzyme, putative:<-->:289454..289845 392 gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 253 End: 342 ............................................................................................................................................................................................................................................................ K H F R M M K P Q M A Q I N M T Q N M L I T D Y V S R L T M .................................................. Protein_Len: 32 Strand: - Start: 139 End: 234 .......................................................................................................................................... L L S I K S S F L K K F I H L P D R K K F L H S H N N L S H H M .............................................................................................................................................................. Protein_Len: 45 Strand: - Start: 84 End: 218 ................................................................................... Y R H S E Y P Q S M R I L L F S D K F C H F K Q H S Y S K L F T Y L I E S K L F I V T I M .............................................................................................................................................................................. gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt 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: 314 End: 343 .........................................................................................................................................................................................................................................................................................................................AATGACACTTCGTTCTGTATATGATACAAT................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 361 End: 390 ........................................................................................................................................................................................................................................................................................................................................................................TGTGACCTCCTTATTAATTTATTTTATTAT.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0296:SSA_0297|SSA_0296:SSA_0297:Transcriptional regulator, XRE family, putative:Malolactic enzyme, putative:<-->:289454..289845 392 gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt Intra-Species Hit: Count: 1 Min: 1 Max: 392 Len: 392 Subject: NC_009009_SSA_0296_SSA_0297|Transcriptional regulator, XRE family, putative:Malolactic enzyme, putative|NEGATIVE:POSITIVE|[289454,289845]|392 HSP 1 e-value: 0.0 bit: 777.0 Len: 392 Query Start:1 Query End:392 Subject Strand: POSITIVE Subject Start: 1 Subject End: 392 gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt gtaaccagaatacaagttttaaatgacaaaaataacaccttaaacaaaacgaagtattttataacaaacatattttggatttagtatctatggctttcatagggctgactcatcctaatgagtaaaaaagagtccttaaagcaatgaaatttttgatgagaataactttttaaaaatgtgtaaaggatctcgctttttaaaaagatgactgtgattatttagggagtgatggataaatgcactattttgttatttatgaaatcgcatcattttcggttgcatagcctgaatattcattgtctgattcattaatattgtatcatatacagaacgaagtgtcatttaatgcaaataagtggtataataaaataaattaataaggaggtcacatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAACCAGAAUACAAGUUUUAAAUGACAAAAAUAACACCUUAAACAAAACGAAGUAUUUUAUAACAAACAUAUUUUGGAUUUAGUAUCUAUGGCUUUCAUAGGGCUGACUCAUCCUAAUGAGUAAAAAAGAGUCCUUAAAGCAAUGAAAUUUUUGAUGAGAAUAACUUUUUAAAAAUGUGUAAAGGAUCUCGCUUUUUAAAAAGAUGACUGUGAUUAUUUAGGGAGUGAUGGAUAAAUGCACUAUUUUGUUAUUUAUGAAAUCGCAUCAUUUUCGGUUGCAUAGCCUGAAUAUUCAUUGUCUGAUUCAUUAAUAUUGUAUCAUAUACAGAACGAAGUGUCAUUUAAUGCAAAUAAGUGGUAUAAUAAAAUAAAUUAAUAAGGAGGUCACAUU ((.(((.........((.((((((((((.....................((((((((.((......)).))))))))......((.(((...(((((...((((((.((((((....)))))).......)))))).))))).((((.((..((((((((.....(((((((((((.(((..........))))))))))))))..(((.((((.((((((((..(..((.((...((((...((((..(.....)..)))).)))).....)).))..)....)))))))).)))).)))...))))))))....)).))))....)))))....)))))))))).))............((((.......)))).......))).))... (-80.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUGACCUCCUUAUUAAUUUAUUUUAUUAUACCACUUAUUUGCAUUAAAUGACACUUCGUUCUGUAUAUGAUACAAUAUUAAUGAAUCAGACAAUGAAUAUUCAGGCUAUGCAACCGAAAAUGAUGCGAUUUCAUAAAUAACAAAAUAGUGCAUUUAUCCAUCACUCCCUAAAUAAUCACAGUCAUCUUUUUAAAAAGCGAGAUCCUUUACACAUUUUUAAAAAGUUAUUCUCAUCAAAAAUUUCAUUGCUUUAAGGACUCUUUUUUACUCAUUAGGAUGAGUCAGCCCUAUGAAAGCCAUAGAUACUAAAUCCAAAAUAUGUUUGUUAUAAAAUACUUCGUUUUGUUUAAGGUGUUAUUUUUGUCAUUUAAAACUUGUAUUCUGGUUAC ...((((((.......((((.......))))...........((((((((((((((.(((((..(((...((((.((.......)).)))).))))))))......((((..((((..((((.(((((.((....((((((.((......))..))))))............................((((((((((((.(.((....)).).).)))))))))))....)).)))))....)))).))))......(((((.((((........)))).)))))...........))))...((((((..(..((((((.(((((......)))))....))))))..)..)))))).....))))))))))....))))....)))))) (-60.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 859 140 91 231 182 NC_009009:SSA_0296|5end_Transcriptional_regulator,_XRE_family,_putative_289363..289593_NEGATIVE 286 286 248 165 132 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 279 115 73 168 130 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 277 112 75 176 136 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 275 120 71 92 46 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 274 310 269 169 130 NC_009009:SSA_2065|5end_hypothetical_protein_2065743..2065973_NEGATIVE 268 110 70 181 134 NC_009009:SSA_2362|5end_L-serine_dehydratase_alpha_subunit_2364708..2364938_POSITIVE 264 125 81 206 149 NC_009009:SSA_0657|5end_PyridoxaL_5'-phosphate_Dependent_Enzymes_class_III,_putative_641445..641675_POSITIVE 263 123 81 173 127 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 252 310 262 111 73 NC_009009:SSA_1892|5end_hypothetical_protein_1889262..1889492_NEGATIVE 251 385 342 204 162 NC_009009:SSA_2190|5end_33_kDa_chaperonin,_putative_2191166..2191396_POSITIVE 250 160 114 71 18 NC_009009:SSA_1991|5end_Pneumococcal_histidine_triad_protein_A,_putative_1988772..1989002_NEGATIVE 249 118 73 171 125 NC_009009:SSA_1055|5end_Conserved_uncharacterized_protein_1070899..1071129_POSITIVE 248 304 262 49 3 NC_009009:SSA_1230|5end_Conserved_uncharacterized_protein_1253358..1253588_NEGATIVE 247 137 92 49 2 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 247 302 261 198 161 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 247 124 87 130 100 NC_009009:SSA_0675|5end_Exodeoxyribonuclease_VII_small_subunit,_putative_658389..658619_POSITIVE 246 124 82 159 112 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 245 137 93 64 1 NC_009009:SSA_1772|5end_hypothetical_protein_1759545..1759775_NEGATIVE 245 309 263 91 41 NC_009009:SSA_0788|5end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_771037..771267_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 135 91 71 14 NC_009009:SSA_2191|3end_Conserved_uncharacterized_protein_2193082..2193232_POSITIVE 283 227 182 79 23 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 275 120 71 95 49 NC_009009:SSA_0852|3end_ATP-dependent_DNA_helicase,_putative_841418..841568_POSITIVE 263 123 81 117 71 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 247 105 75 145 114 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 245 137 93 74 11 NC_009009:SSA_1773|3end_hypothetical_protein_1759535..1759685_NEGATIVE 245 309 263 52 2 NC_009009:SSA_0787|3end_Proton-translocating_ATPase,_F1_sector,_gamma_subunit,_putative_771078..771228_POSITIVE 244 135 91 97 50 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 241 302 262 149 108 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 240 117 80 84 51 NC_009009:SSA_2257|3end_DNA_mismatch_repair_protein,_putative_2251241..2251391_NEGATIVE 238 116 71 139 92 NC_009009:SSA_0386|3end_Glycine-betaine_ABC_transporter,_ATPase_component,_putative_380265..380415_NEGATIVE 238 114 77 92 53 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 237 117 73 115 69 NC_009009:SSA_0952|3end_hypothetical_protein_958095..958245_POSITIVE 236 307 263 111 60 NC_009009:SSA_1303|3end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322474..1322624_NEGATIVE 236 123 87 151 122 NC_009009:SSA_0674|3end_Exodeoxyribonuclease_VII_large_subunit,_putative_658491..658641_POSITIVE 235 135 95 150 109 NC_009009:SSA_0871|3end_Cell_division_protein_FtsX,_putative_864627..864777_POSITIVE 235 116 76 143 110 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 233 300 264 90 47 NC_009009:SSA_0701|3end_Cation_transporter_CorA_family,_putative_685356..685506_POSITIVE 233 115 77 78 44 NC_009009:SSA_0577|3end_Ancient_RNA-binding_IF3-C_fold_(CRS1/YhbY_domain),_putative_571644..571794_POSITIVE 233 307 261 123 68 NC_009009:SSA_0316|3end_hypothetical_protein_311342..311492_POSITIVE