Origin IGS: tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca .........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 tgttgacctccattgataaattaatagcattattataccactaaagaaaaaggaagtccatagaaaataaaagcaatattgtaagaaggttgttttcctgtttacagagaaaaggcaaaccctgatatggaagcagcatgctcttattcggtttctttggaaaattttcccttttcatatgataaatcgctaaaaaatgtagaaaaacattctgcatgacttgcaatttttttcaaaaatgttatcatagtagaaagctttttgaatttttagaaaattgtaaataaatgaaaggggaaga Mask Tandem Repeat Region ================================================ tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca Find is-nt database================================================ Query_seq: SSA_1970:SSA_1971|SSA_1970:SSA_1971:Acetolactate synthase, large subunit, biosynthetic type, putative:hypothetical protein:<-->:1967006..1967306 301 tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1970:SSA_1971|SSA_1970:SSA_1971:Acetolactate synthase, large subunit, biosynthetic type, putative:hypothetical protein:<-->:1967006..1967306 301 tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1970:SSA_1971|SSA_1970:SSA_1971:Acetolactate synthase, large subunit, biosynthetic type, putative:hypothetical protein:<-->:1967006..1967306 301 tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 17 End: 109 ................ M Y N F L K I Q K A F Y Y D N I F E K N C K S C R M F F Y I F ................................................................................................................................................................................................ Protein_Len: 34 Strand: + Start: 54 End: 155 ..................................................... M I T F L K K I A S H A E C F S T F F S D L S Y E K G K F S K E T E .................................................................................................................................................. Protein_Len: 60 Strand: + Start: 76 End: 258 ........................................................................... M Q V M Q N V F L H F L A I Y H M K R E N F P K K P N K S M L L P Y Q G L P F L C K Q E N N L L T I L L L F S M D F L F ........................................... Protein_Len: 55 Strand: + Start: 137 End: 301 ........................................................................................................................................ M F Q R N R I R A C C F H I R V C L F S V N R K T T F L Q Y C F Y F L W T S F F F S G I I M L L I Y Q W R S T Protein_Len: 31 Strand: - Start: 112 End: 204 ............................................................................................................... R N I M H F P F I K W L F R I L A H Q K W I L T Q R K E T F M ................................................................................................. Protein_Len: 30 Strand: - Start: 86 End: 175 ..................................................................................... A S H K E V N K L S K D Y S F P F N E L S V S Y S C A A E M .............................................................................................................................. Protein_Len: 33 Strand: - Start: 18 End: 116 ................. K C N E L F E F L K R S H Y C K Q F F N C T M C F T K R C K K A M ......................................................................................................................................................................................... tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca 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: 85 Start: 241 End: 270 ................................................................................................................................................................................................................................................ATGGACTTCCTTTTTCTTTAGTGGTATAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -3.9 Tail_Score: -2.57162 Start: 86 End: 104 Full_Region: taaatcgctaaaaaa tgtagaa aaaca ttctgca tgacttgcaattttt .....................................................................................tgtagaaaaacattctgca..................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1970:SSA_1971|SSA_1970:SSA_1971:Acetolactate synthase, large subunit, biosynthetic type, putative:hypothetical protein:<-->:1967006..1967306 301 tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca Intra-Species Hit: Count: 1 Min: 1 Max: 301 Len: 301 Subject: NC_009009_SSA_1970_SSA_1971|Acetolactate synthase, large subunit, biosynthetic type, putative:hypothetical protein|NEGATIVE:POSITIVE|[1967006,1967306]|301 HSP 1 e-value: 1.0E-157 bit: 555.0 Len: 301 Query Start:1 Query End:301 Subject Strand: POSITIVE Subject Start: 1 Subject End: 301 tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgnnnnnnnttgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca tcttcccctttcatttatttacaattttctaaaaattcaaaaagctttctactatgataacatttttgaaaaaaattgcaagtcatgcagaatgtttttctacattttttagcgatttatcatatgaaaagggaaaattttccaaagaaaccgaataagagcatgctgcttccatatcagggtttgccttttctctgtaaacaggaaaacaaccttcttacaatattgcttttattttctatggacttcctttttctttagtggtataataatgctattaatttatcaatggaggtcaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUCCCCUUUCAUUUAUUUACAAUUUUCUAAAAAUUCAAAAAGCUUUCUACUAUGAUAACAUUUUUGAAAAAAAUUGCAAGUCAUGCAGAAUGUUUUUCUACAUUUUUUAGCGAUUUAUCAUAUGAAAAGGGAAAAUUUUCCAAAGAAACCGAAUAAGAGCAUGCUGCUUCCAUAUCAGGGUUUGCCUUUUCUCUGUAAACAGGAAAACAACCUUCUUACAAUAUUGCUUUUAUUUUCUAUGGACUUCCUUUUUCUUUAGUGGUAUAAUAAUGCUAUUAAUUUAUCAAUGGAGGUCAACA ..(((((.((((((.....................((((((((....((......)).....))))))))..((((((((((..(((.((((.....)))).)))..))).))))))).....)))))).))))).......((.(((....(((((((((((....((.(((......)))...)).(((((.(((....)))))))).................)))))))))))))).))(((((((.......((((((((((....)))))))))).........))))))).... (-66.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUGACCUCCAUUGAUAAAUUAAUAGCAUUAUUAUACCACUAAAGAAAAAGGAAGUCCAUAGAAAAUAAAAGCAAUAUUGUAAGAAGGUUGUUUUCCUGUUUACAGAGAAAAGGCAAACCCUGAUAUGGAAGCAGCAUGCUCUUAUUCGGUUUCUUUGGAAAAUUUUCCCUUUUCAUAUGAUAAAUCGCUAAAAAAUGUAGAAAAACAUUCUGCAUGACUUGCAAUUUUUUUCAAAAAUGUUAUCAUAGUAGAAAGCUUUUUGAAUUUUUAGAAAAUUGUAAAUAAAUGAAAGGGGAAGA (((..(......)..)))......................(((((((((..(((..((((((..........(((....))).....((((.((((((((....))).)))))....))))....)))))).((.....)).....)))..)))))))))....((((((((((((((..................((((((((.....))))))))...(((((((((((((((((((.(((.((......)).)))))))))))......)))))))))))....)))))))))))))) (-67.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 733 90 41 181 132 NC_009009:SSA_1970|5end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1966915..1967145_NEGATIVE 327 197 160 111 77 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 314 199 156 164 119 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 312 199 151 231 178 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 311 197 151 68 20 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 307 200 152 87 37 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 306 198 153 49 2 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 294 218 171 179 131 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 291 173 133 68 28 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 290 197 159 86 38 NC_009009:SSA_1028|5end_Transcriptional_repressor,_XRE_family,_putative_1046063..1046293_NEGATIVE 290 197 151 50 9 NC_009009:SSA_0885|5end_hypothetical_protein_879514..879744_NEGATIVE 287 195 152 164 113 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 284 169 131 68 34 NC_009009:SSA_1568|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571200..1571430_POSITIVE 284 189 162 30 4 NC_009009:SSA_0079|5end_ROK_family_protein,_putative_82855..83085_POSITIVE 282 186 157 213 183 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 279 206 161 226 181 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 276 204 161 125 70 NC_009009:SSA_0503|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_502231..502461_POSITIVE 275 197 161 140 93 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 274 185 151 78 36 NC_009009:SSA_2199|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2201108..2201338_NEGATIVE 274 168 131 69 18 NC_009009:SSA_1111|5end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1136532..1136762_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 197 160 121 87 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 311 197 151 56 8 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 307 200 152 90 40 NC_009009:SSA_0316|3end_hypothetical_protein_311342..311492_POSITIVE 306 198 153 62 15 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 284 169 131 55 21 NC_009009:SSA_1567|3end_Polar_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_1571267..1571417_POSITIVE 276 204 161 137 82 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 274 185 151 77 35 NC_009009:SSA_2200|3end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201109..2201259_NEGATIVE 272 189 141 61 21 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 270 195 153 68 29 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 267 197 152 83 28 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 265 198 159 133 82 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 262 206 162 111 67 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 261 194 164 69 41 NC_009009:SSA_1529|3end_Lysyl-tRNA_synthetase,_putative_1537441..1537591_POSITIVE 260 197 157 139 101 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 257 118 73 100 58 NC_009009:SSA_0654|3end_Cell_division_protein_DivIB,_putative_638742..638892_POSITIVE 256 195 152 111 48 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 255 187 151 130 96 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 255 185 157 151 122 NC_009009:SSA_1633|3end_FimA_fimbrial_subunit-like_protein,_putative_1634106..1634256_NEGATIVE 248 198 159 83 38 NC_009009:SSA_2022|3end_Transcriptional_regulator,_MerR_family_(multidrug-efflux_transporter_genes),_putative_2024488..2024638_POSITIVE 248 199 160 111 60 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE