Origin IGS: atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat .........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 atctttctcctttgtgttagataatatgacatagattttaccatagaataaataaactgtcaaattgaataaaaatgactattttccttcagagaaaaatttttttgatgagaatcgtccgttttctacaaatgtggaacaaaaatggcttgaattagtgttttttaagaaaactttggtataataagactatataaataaataaaattggattgggagtctagctaggcaaactagattgccttttgcacgttttgatgcaggacgacttagctgactatgtcacaacttttctatcatggagttgattcaatcccaatcttatgttaaggtgaacat Mask Tandem Repeat Region ================================================ atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat Find is-nt database================================================ Query_seq: SSA_1565:SSA_1566|SSA_1565:SSA_1566:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:Polar amino acid ABC transporter, ATP-binding protein, putative:<-->:1569400..1569738 339 atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1565:SSA_1566|SSA_1565:SSA_1566:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:Polar amino acid ABC transporter, ATP-binding protein, putative:<-->:1569400..1569738 339 atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1565:SSA_1566|SSA_1565:SSA_1566:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:Polar amino acid ABC transporter, ATP-binding protein, putative:<-->:1569400..1569738 339 atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 159 End: 275 .............................................................................................................................................................. V L T K K F F V L E L W K Q E V N T S F P R N E D F F N K E S P F Y D N K N M ................................................................ atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat 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: 93 Start: 276 End: 305 ...................................................................................................................................................................................................................................................................................TTTGACAGTTTATTTATTCTATGGTAAAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 62 HP_score: -4.7 Tail_Score: -4.19276 Start: 97 End: 112 Full_Region: ttgggagtctagcta ggcaa actaga ttgcc ttttgcacgttttga ................................................................................................ggcaaactagattgcc................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1565:SSA_1566|SSA_1565:SSA_1566:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:Polar amino acid ABC transporter, ATP-binding protein, putative:<-->:1569400..1569738 339 atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat Intra-Species Hit: Count: 1 Min: 1 Max: 339 Len: 339 Subject: NC_009009_SSA_1565_SSA_1566|Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:Polar amino acid ABC transporter, ATP-binding protein, putative|NEGATIVE:POSITIVE|[1569400,1569738]|339 HSP 1 e-value: 1.0E-180 bit: 630.0 Len: 339 Query Start:1 Query End:339 Subject Strand: POSITIVE Subject Start: 1 Subject End: 339 atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcnnnnnnntttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat atgttcaccttaacataagattgggattgaatcaactccatgatagaaaagttgtgacatagtcagctaagtcgtcctgcatcaaaacgtgcaaaaggcaatctagtttgcctagctagactcccaatccaattttatttatttatatagtcttattataccaaagttttcttaaaaaacactaattcaagccatttttgttccacatttgtagaaaacggacgattctcatcaaaaaaatttttctctgaaggaaaatagtcatttttattcaatttgacagtttatttattctatggtaaaatctatgtcatattatctaacacaaaggagaaagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUUCACCUUAACAUAAGAUUGGGAUUGAAUCAACUCCAUGAUAGAAAAGUUGUGACAUAGUCAGCUAAGUCGUCCUGCAUCAAAACGUGCAAAAGGCAAUCUAGUUUGCCUAGCUAGACUCCCAAUCCAAUUUUAUUUAUUUAUAUAGUCUUAUUAUACCAAAGUUUUCUUAAAAAACACUAAUUCAAGCCAUUUUUGUUCCACAUUUGUAGAAAACGGACGAUUCUCAUCAAAAAAAUUUUUCUCUGAAGGAAAAUAGUCAUUUUUAUUCAAUUUGACAGUUUAUUUAUUCUAUGGUAAAAUCUAUGUCAUAUUAUCUAACACAAAGGAGAAAGAU ...(((.((((..........(((..(((...)))..)))...((((.....((((((((((.......((((((((.((((......))))....(((..(((((((.....))))))).............................................(((((.....)))))..........))).......(((.((....)).)))...))))))))...((((.....((((((((....)))))))).((((..((.....))..))))...............)))).....))))))))))...)))).....)))).))).... (-61.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUUCUCCUUUGUGUUAGAUAAUAUGACAUAGAUUUUACCAUAGAAUAAAUAAACUGUCAAAUUGAAUAAAAAUGACUAUUUUCCUUCAGAGAAAAAUUUUUUUGAUGAGAAUCGUCCGUUUUCUACAAAUGUGGAACAAAAAUGGCUUGAAUUAGUGUUUUUUAAGAAAACUUUGGUAUAAUAAGACUAUAUAAAUAAAUAAAAUUGGAUUGGGAGUCUAGCUAGGCAAACUAGAUUGCCUUUUGCACGUUUUGAUGCAGGACGACUUAGCUGACUAUGUCACAACUUUUCUAUCAUGGAGUUGAUUCAAUCCCAAUCUUAUGUUAAGGUGAACAU ..........(((((((((.......))))))))).((((((.(((............((((..............(((.((((((..((((((((....)))))))).)))))).)))....((((((....))))))......))))....(((((.((((((...)))))).))))).........)))..........(((....((((((((((((.((((((((((......))))).......(((((((...)))))))...)))))))).......(((((((........)))))))......)))))))))....))).))))))... (-74.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 946 120 71 211 162 NC_009009:SSA_1565|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1569309..1569539_NEGATIVE 387 95 51 223 185 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 349 99 51 79 24 NC_009009:SSA_0709|5end_hypothetical_protein_695895..696125_NEGATIVE 321 100 58 52 13 NC_009009:SSA_1960|5end_hypothetical_protein_1958466..1958696_NEGATIVE 313 85 45 186 150 NC_009009:SSA_0878|5end_DNA_gyrase,_putative_871596..871826_POSITIVE 313 110 61 199 148 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 312 83 51 161 124 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 305 129 81 53 11 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 297 120 71 172 124 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 296 132 91 189 139 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 293 109 62 41 2 NC_009009:SSA_1938|5end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1925738..1925968_NEGATIVE 290 104 61 213 164 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 279 126 88 66 19 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 279 80 37 193 147 NC_009009:SSA_0287|5end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_279528..279758_POSITIVE 277 99 51 48 8 NC_009009:SSA_0871|5end_Cell_division_protein_FtsX,_putative_863621..863851_POSITIVE 275 120 71 59 15 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 275 116 74 62 20 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 273 130 90 146 112 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 273 98 51 161 124 NC_009009:SSA_0729|5end_hypothetical_protein_714397..714627_POSITIVE 272 119 76 160 119 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 99 51 89 34 NC_009009:SSA_0711|3end_hypothetical_protein_695885..696035_NEGATIVE 305 129 81 43 1 NC_009009:SSA_0238|3end_hypothetical_protein_233031..233181_POSITIVE 298 100 51 148 103 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE 281 66 23 132 96 NC_009009:SSA_0841|3end_hypothetical_protein_827236..827386_POSITIVE 280 121 96 42 15 NC_009009:SSA_0153|3end_hypothetical_protein_149503..149653_POSITIVE 279 80 37 147 101 NC_009009:SSA_0286|3end_Transaldolase-like_protein,_putative_279562..279712_POSITIVE 277 99 51 55 15 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 275 120 71 66 22 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 275 116 74 50 8 NC_009009:SSA_0420|3end_Hydrolase,_HAD_superfamily,_putative_419632..419782_POSITIVE 274 65 24 151 113 NC_009009:SSA_1932|3end_Biotin_carboxylase,_putative_1919507..1919657_NEGATIVE 273 122 81 135 98 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 266 103 62 151 109 NC_009009:SSA_0222|3end_PTS_system,_mannose-specific_IID_component,_putative_218133..218283_POSITIVE 265 119 71 148 112 NC_009009:SSA_0768|3end_Ribonucleoside-diphosphate_reductase_2,_beta_subunit,_putative_748136..748286_NEGATIVE 264 108 61 146 89 NC_009009:SSA_2012|3end_hypothetical_protein_2012898..2013048_NEGATIVE 264 80 37 149 97 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 261 126 90 149 119 NC_009009:SSA_1526|3end_hypothetical_protein_1534674..1534824_POSITIVE 260 80 31 150 107 NC_009009:SSA_2268|3end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_2269386..2269536_POSITIVE 259 120 74 77 36 NC_009009:SSA_1357|3end_hypothetical_protein_1372077..1372227_NEGATIVE 257 108 61 56 7 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 252 99 53 48 9 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE