Origin IGS: gtaactagaaaaaaatgtaaaataattttttttaatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat .........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 atgtcaggttgaagcgggtgttatgtgttaattttcaatttcccttttaaataaaattataagcaaaacttttatatcttaatagttcgattaaattcttgcccccactcttttagctaaatatccaaaacttgattatcatcatcatacatattaaaaaaaattattttacatttttttctagttac Mask Tandem Repeat Region ================================================ gtaactagaaaaaaatgtaaaataattttttttaatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat Find is-nt database================================================ Query_seq: TDE0586:TDE0587|TDE0586:TDE0587:hypothetical protein:hypothetical protein:->->:625701..625888 188 gtaactagaaaaaaatgtaaaataattttttttaatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0586:TDE0587|TDE0586:TDE0587:hypothetical protein:hypothetical protein:->->:625701..625888 188 gtaactagaaaaaaatgtaaaataattttttttaatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0586:TDE0587|TDE0586:TDE0587:hypothetical protein:hypothetical protein:->->:625701..625888 188 gtaactagaaaaaaatgtaaaataattttttttaatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaactagaaaaaaatgtaaaataattttttttaatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat Predict ORF larger than 30AA ================================================ gtaactagaaaaaaatgtaaaataattttttttaatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat 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================================================ gtaactagaaaaaaatgtaaaataattttttttaatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0586:TDE0587|TDE0586:TDE0587:hypothetical protein:hypothetical protein:->->:625701..625888 188 gtaactagaaaaaaatgtaaaataattttttttaatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat Intra-Species Hit: Count: 1 Min: 34 Max: 188 Len: 155 Subject: NC_002967_TDE0586_TDE0587|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[625701,625888]|188 HSP 1 e-value: 7.0E-83 bit: 307.0 Len: 155 Query Start:34 Query End:188 Subject Strand: POSITIVE Subject Start: 34 Subject End: 188 .................................aatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat .................................aatatgtatgatgatgataatcaagttttggatatttagctaaaagagtgggggcaagaatttaatcgaactattaagatataaaagttttgcttataattttatttaaaagggaaattgaaaattaacacataacacccgcttcaacctgacat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUGUAUGAUGAUGAUAAUCAAGUUUUGGAUAUUUAGCUAAAAGAGUGGGGGCAAGAAUUUAAUCGAACUAUUAAGAUAUAAAAGUUUUGCUUAUAAUUUUAUUUAAAAGGGAAAUUGAAAAUUAACACAUAACACCCGCUUCAACCUGACAU ...((((....((((....))))..((((((........))))))(((((((.((((((.(((((((..........))).))))..))))))...(((((((..........))))))).................))))))).......)))) (-21.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUCAGGUUGAAGCGGGUGUUAUGUGUUAAUUUUCAAUUUCCCUUUUAAAUAAAAUUAUAAGCAAAACUUUUAUAUCUUAAUAGUUCGAUUAAAUUCUUGCCCCCACUCUUUUAGCUAAAUAUCCAAAACUUGAUUAUCAUCAUCAUACAUAUU ..((((((((.....(((((((......(((((((..((((.......)))))))))))..(((..((((.(((.....))).)))).((......)).................))).)))))))..))))))))................... (-16.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 150 107 70 30 NC_002967:TDE1824|5end_hypothetical_protein_1857011..1857241_POSITIVE 321 88 46 221 165 NC_002967:TDE2052|5end_aminotransferase,_class_V_2080402..2080632_POSITIVE 253 143 106 43 4 NC_002967:TDE2060|5end_hypothetical_protein_2086521..2086751_POSITIVE 240 68 23 175 121 NC_002967:TDE0604|5end_hypothetical_protein_642631..642861_NEGATIVE 233 70 23 103 48 NC_002967:TDE2621|5end_hypothetical_protein_2661971..2662201_POSITIVE 232 55 22 58 27 NC_002967:TDE0646|5end_hypothetical_protein_681865..682095_NEGATIVE 227 79 31 93 40 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 221 60 41 223 200 NC_002967:TDE0434|5end_rubrerythrin_488909..489139_POSITIVE 217 72 50 209 180 NC_002967:TDE2692|5end_CTP_synthetase_2729421..2729651_POSITIVE 209 58 29 153 122 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 208 58 15 198 162 NC_002967:TDE0089|5end_transglutaminase-like_domain_protein_108554..108784_NEGATIVE 206 60 14 156 107 NC_002967:TDE2381|5end_histidine_kinase-related_ATPase,_putative_2411069..2411299_POSITIVE 205 69 22 57 14 NC_002967:TDE0963|5end_DNA_polymerase_IV_985895..986125_POSITIVE 204 70 26 95 49 NC_002967:TDE0912|5end_hypothetical_protein_931350..931580_POSITIVE 203 53 15 86 45 NC_002967:TDE0855|5end_DNA-binding_response_regulator_876536..876766_POSITIVE 202 64 25 224 188 NC_002967:TDE2465|5end_hypothetical_protein_2489651..2489881_NEGATIVE 202 79 43 231 181 NC_002967:TDE2104|5end_hypothetical_protein_2131083..2131313_NEGATIVE 201 59 18 189 152 NC_002967:TDE2655|5end_hypothetical_protein_2693070..2693300_NEGATIVE 200 72 36 73 39 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 200 149 113 50 22 NC_002967:TDE1374|5end_hypothetical_protein_1417998..1418228_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 146 109 69 32 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 233 70 23 89 34 NC_002967:TDE2620|3end_hypothetical_protein_2662037..2662187_POSITIVE 227 79 31 109 56 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 219 63 21 69 26 NC_002967:TDE2142|3end_methyl-accepting_chemotaxis_protein_2177987..2178137_POSITIVE 218 150 127 51 26 NC_002967:TDE0098|3end_hypothetical_protein_114842..114992_NEGATIVE 217 72 50 54 25 NC_002967:TDE2691|3end_hypothetical_protein_2729346..2729496_POSITIVE 213 150 105 62 12 NC_002967:TDE2760|3end_flagellar_biosynthesis_protein_2815066..2815216_NEGATIVE 209 58 29 147 116 NC_002967:TDE2233|3end_iron_compound_ABC_transporter,_permease_protein,_putative_2271291..2271441_NEGATIVE 206 60 14 69 20 NC_002967:TDE2380|3end_hypothetical_protein_2411062..2411212_POSITIVE 205 60 28 34 1 NC_002967:TDE1724|3end_hypothetical_protein_1778371..1778521_POSITIVE 205 69 22 55 12 NC_002967:TDE0962|3end_hypothetical_protein_985973..986123_POSITIVE 202 79 43 108 58 NC_002967:TDE2105|3end_hypothetical_protein_2131206..2131356_NEGATIVE 202 68 21 40 3 NC_002967:TDE1636|3end_surface_antigen,_putative_1683517..1683667_NEGATIVE 200 72 36 60 26 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 198 60 15 129 76 NC_002967:TDE1994|3end_hypothetical_protein_2012342..2012492_NEGATIVE 197 58 12 151 99 NC_002967:TDE2308|3end_hypothetical_protein_2346313..2346463_POSITIVE 196 59 23 54 22 NC_002967:TDE2491|3end_DNA_polymerase_domain_protein_2514705..2514855_NEGATIVE 196 70 28 46 6 NC_002967:TDE1755|3end_hypothetical_protein_1807187..1807337_POSITIVE 193 58 22 141 109 NC_002967:TDE2754|3end_ornithine_cyclodeaminase_2810761..2810911_NEGATIVE 193 68 24 148 103 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE