Origin IGS: attgattctcctttctaattttttctaaatcaaaattgtttaataatattttttactattattttttgattaacataattatataattttccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta .........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 taaaatattatctttctttatatagtgtttttattatcaggcaattataccatattttatgcatttaacctcgtttaacaactctaaaatatatctaaaaatgctgataaaagcctatagaacaaggaattcttatctttgcgtatctatagtacagataaacggaaagaaaactaagttgaattattatgtttccaagttggaaaattatataattatgttaatcaaaaaataatagtaaaaaatattattaaacaattttgatttagaaaaaattagaaaggagaatcaat Mask Tandem Repeat Region ================================================ attgattctcctttctaattttttctaaatcaaaattgtttaataatattttttactattattttttgattaacataattatataattttccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta Find is-nt database================================================ Query_seq: SSA_2150:SSA_2151|SSA_2150:SSA_2151:hypothetical protein:M protein trans-acting positive transcriptional regulator (MGA), putative:<-->:2151207..2151499 293 attgattctcctttctaattttttctaaatcaaaattgtttaataatattttttactattattttttgattaacataattatataattttccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2150:SSA_2151|SSA_2150:SSA_2151:hypothetical protein:M protein trans-acting positive transcriptional regulator (MGA), putative:<-->:2151207..2151499 293 attgattctcctttctaattttttctaaatcaaaattgtttaataatattttttactattattttttgattaacataattatataattttccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2150:SSA_2151|SSA_2150:SSA_2151:hypothetical protein:M protein trans-acting positive transcriptional regulator (MGA), putative:<-->:2151207..2151499 293 attgattctcctttctaattttttctaaatcaaaattgtttaataatattttttactattattttttgattaacataattatataattttccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attgattctcctttctaattttttctaaatcaaaattgtttaataatattttttactattattttttgattaacataattatataattttccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 83 End: 196 .................................................................................. M I F Q L G N I I I Q L S F L S V Y L Y Y R Y A K I R I P C S I G F Y Q H F ................................................................................................. Protein_Len: 60 Strand: - Start: 62 End: 250 ............................................................. L M I I Y N E L K S V Y Y N L K T K K G N I Q V I S V C L Y S N R T R Y A K I L M K L Y I K S N N F S T L H M F Y P I M ........................................... attgattctcctttctaattttttctaaatcaaaattgtttaataatattttttactattattttttgattaacataattatataattttccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attgattctcctttctaattttttctaaatcaaaattgtttaataatattttttactattattttttgattaacataattatataattttccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2150:SSA_2151|SSA_2150:SSA_2151:hypothetical protein:M protein trans-acting positive transcriptional regulator (MGA), putative:<-->:2151207..2151499 293 attgattctcctttctaattttttctaaatcaaaattgtttaataatattttttactattattttttgattaacataattatataattttccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta Intra-Species Hit: Count: 1 Min: 91 Max: 293 Len: 203 Subject: NC_009009_SSA_2150_SSA_2151|hypothetical protein:M protein trans-acting positive transcriptional regulator (MGA), putative|NEGATIVE:POSITIVE|[2151207,2151499]|293 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 203 Query Start:91 Query End:293 Subject Strand: POSITIVE Subject Start: 91 Subject End: 293 ..........................................................................................ccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta ..........................................................................................ccaacttggaaacataataattcaacttagttttctttccgtttatctgtactatagatacgcaaagataagaattccttgttctataggcttttatcagcatttttagatatattttagagttgttaaacgaggttaaatgcataaaatatggtataattgcctgataataaaaacactatataaagaaagataatatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAACUUGGAAACAUAAUAAUUCAACUUAGUUUUCUUUCCGUUUAUCUGUACUAUAGAUACGCAAAGAUAAGAAUUCCUUGUUCUAUAGGCUUUUAUCAGCAUUUUUAGAUAUAUUUUAGAGUUGUUAAACGAGGUUAAAUGCAUAAAAUAUGGUAUAAUUGCCUGAUAAUAAAAACACUAUAUAAAGAAAGAUAAUAUUUUA ......((....))...............(((.((((((............(((((((...((((.((.......)).)))))))))))....(((((((((...(((..(((((((((..((..((((......))))..)).)))))))))...))).)).))))))).................)))))).)))...... (-33.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAUUAUCUUUCUUUAUAUAGUGUUUUUAUUAUCAGGCAAUUAUACCAUAUUUUAUGCAUUUAACCUCGUUUAACAACUCUAAAAUAUAUCUAAAAAUGCUGAUAAAAGCCUAUAGAACAAGGAAUUCUUAUCUUUGCGUAUCUAUAGUACAGAUAAACGGAAAGAAAACUAAGUUGAAUUAUUAUGUUUCCAAGUUGG ..........(((((((...(((((.(((((((((....((((.((.((..((((((((.....((((......))))......))))))))...)).)).)))))))))))))))))).............((((((.(((.........))).))))))..)))))))...((((.(((..............))).)))) (-29.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 747 50 1 231 182 NC_009009:SSA_2150|5end_hypothetical_protein_2151116..2151346_NEGATIVE 294 92 54 62 15 NC_009009:SSA_2039|5end_Aminoacid_specific_permease,_putative_2044455..2044685_NEGATIVE 287 123 89 177 137 NC_009009:SSA_1491|5end_Methionine_aminopeptidase_A,_putative_1497637..1497867_NEGATIVE 266 68 22 208 158 NC_009009:SSA_0988|5end_TfoX_N-terminal_domain_family_protein,_putative_990662..990892_POSITIVE 263 113 72 114 70 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 252 101 61 129 86 NC_009009:SSA_1953|5end_NifU_family_protein,_putative_1950079..1950309_NEGATIVE 252 80 33 81 26 NC_009009:SSA_0315|5end_Transcriptional_regulator,_MarR_family,_putative_310102..310332_POSITIVE 248 92 56 203 164 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 245 126 82 72 13 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 244 112 75 48 17 NC_009009:SSA_1537|5end_Conserved_uncharacterized_protein_1544441..1544671_NEGATIVE 243 91 52 141 102 NC_009009:SSA_0755|5end_hypothetical_protein_736212..736442_POSITIVE 242 113 78 155 114 NC_009009:SSA_1700|5end_hypothetical_protein_1691288..1691518_NEGATIVE 242 100 55 200 136 NC_009009:SSA_0529|5end_Ethanolamine_utilization_protein,_putative_525945..526175_POSITIVE 236 78 34 137 96 NC_009009:SSA_0191|5end_Adenine-specific_DNA_methylase,_putative_191907..192137_POSITIVE 232 103 75 122 92 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 231 127 88 223 180 NC_009009:SSA_0855|5end_O-acetylhomoserine_sulfhydrylase,_putative_841832..842062_POSITIVE 228 135 91 151 104 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 225 100 54 166 113 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 222 89 45 187 149 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 222 64 25 126 92 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 109 61 68 19 NC_009009:SSA_1878|3end_Conserved_uncharacterized_protein_1871943..1872093_NEGATIVE 266 68 22 60 10 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 263 113 72 80 36 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 252 101 61 142 99 NC_009009:SSA_1954|3end_Aminotransferase,_class-V,_putative_1950066..1950216_NEGATIVE 242 113 78 144 103 NC_009009:SSA_1701|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1691299..1691449_NEGATIVE 236 78 34 55 14 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 234 107 61 78 40 NC_009009:SSA_2196|3end_Conserved_uncharacterized_protein_2196929..2197079_NEGATIVE 231 127 88 124 81 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE 228 135 91 132 85 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 224 119 79 151 111 NC_009009:SSA_1492|3end_hypothetical_protein_1497659..1497809_NEGATIVE 222 89 45 135 97 NC_009009:SSA_1987|3end_hypothetical_protein_1982583..1982733_NEGATIVE 222 64 25 104 70 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 220 69 30 132 90 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 219 105 61 148 99 NC_009009:SSA_0143|3end_Conserved_uncharacterized_protein_137880..138030_POSITIVE 214 92 66 32 4 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 214 99 54 79 32 NC_009009:SSA_1515|3end_hypothetical_protein_1521770..1521920_NEGATIVE 211 94 51 108 51 NC_009009:SSA_1959|3end_Undecaprenyl-diphosphatase,_putative_1955589..1955739_NEGATIVE 211 106 61 149 111 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 210 110 64 80 31 NC_009009:SSA_2345|3end_hypothetical_protein_2347502..2347652_POSITIVE 210 62 31 138 109 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE