Origin IGS: actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatagaaaaaaag .........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 ctttttttctatcgaaacaaaataaaatctttcatttgaaccataggattcatcatcaggtatataatcataaacggaaatgtccgaaatatcataatattccgagtataaactatcggcatattttttaaaaaaaatctcttcttttgaattttcctgtttaggttttgactttatgcttacatcatgtttacttaaacctgattttccttctttaaattcttttattataggatacagt Mask Tandem Repeat Region ================================================ actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatagaaaaaaag Find is-nt database================================================ Query_seq: TDE0458:TDE0459|TDE0458:TDE0459:hypothetical protein:hypothetical protein:->->:514281..514521 241 actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatagaaaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0458:TDE0459|TDE0458:TDE0459:hypothetical protein:hypothetical protein:->->:514281..514521 241 actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatagaaaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0458:TDE0459|TDE0458:TDE0459:hypothetical protein:hypothetical protein:->->:514281..514521 241 actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatagaaaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatagaaaaaaag Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 90 End: 230 ......................................................................................... M Q K K R F F L K N M P I V Y T R N I M I F R T F P F M I I Y L M M N P M V Q M K D F I L F R ........... Protein_Len: 60 Strand: + Start: 2 End: 241 . M Y P I I K E F K E G K S G L S K H D V S I K S K P K Q E N S K E E I F F K K Y A D S L Y S E Y Y D I S D I S V Y D Y I Protein_Len: 34 Strand: - Start: 114 End: 215 ................................................................................................................. F I H R Y N I S P I N H Y K P C K R K H N Y V Q H H I R H N L H F M .......................... Protein_Len: 35 Strand: - Start: 1 End: 105 S Y G I I F S N L S P F D P K L L C S T L M F D F G L C S F E F S S M ........................................................................................................................................ actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatagaaaaaaag 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: 84 Start: 146 End: 175 .................................................................................................................................................TATGATATTTCGGACATTTCCGTTTATGAT.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatagaaaaaaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0458:TDE0459|TDE0458:TDE0459:hypothetical protein:hypothetical protein:->->:514281..514521 241 actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatagaaaaaaag Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: NC_002967_TDE0458_TDE0459|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[514281,514521]|241 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 233 Query Start:1 Query End:233 Subject Strand: POSITIVE Subject Start: 1 Subject End: 233 actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagannnnnnnnaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatag........ actgtatcctataataaaagaatttaaagaaggaaaatcaggtttaagtaaacatgatgtaagcataaagtcaaaacctaaacaggaaaattcaaaagaagagattttttttaaaaaatatgccgatagtttatactcggaatattatgatatttcggacatttccgtttatgattatatacctgatgatgaatcctatggttcaaatgaaagattttattttgtttcgatag........ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGUAUCCUAUAAUAAAAGAAUUUAAAGAAGGAAAAUCAGGUUUAAGUAAACAUGAUGUAAGCAUAAAGUCAAAACCUAAACAGGAAAAUUCAAAAGAAGAGAUUUUUUUUAAAAAAUAUGCCGAUAGUUUAUACUCGGAAUAUUAUGAUAUUUCGGACAUUUCCGUUUAUGAUUAUAUACCUGAUGAUGAAUCCUAUGGUUCAAAUGAAAGAUUUUAUUUUGUUUCGAUAG ....((((....(((((((((((((...........(((((((.(((((((((..(((((..(((((.........(((....))).......(((((((....))))))).......)))))..............((((((((....)))))))).)))))...))))))..)))...)))))))..((((((....))))))......))))))..)))))))..)))). (-39.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUCGAAACAAAAUAAAAUCUUUCAUUUGAACCAUAGGAUUCAUCAUCAGGUAUAUAAUCAUAAACGGAAAUGUCCGAAAUAUCAUAAUAUUCCGAGUAUAAACUAUCGGCAUAUUUUUUAAAAAAAAUCUCUUCUUUUGAAUUUUCCUGUUUAGGUUUUGACUUUAUGCUUACAUCAUGUUUACUUAAACCUGAUUUUCCUUCUUUAAAUUCUUUUAUUAUAGGAUACAGU ...(((((((............(((....)))..((((((....(((..(((..............((((....)))).........(((((.((((..........)))).))))).................)))..)))....))))))....)))))))............((((.((((....)))).))))..((((....((((....))))....))))...... (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 168 121 222 180 NC_002967:TDE0190|5end_hypothetical_protein_227366..227596_NEGATIVE 257 150 121 133 100 NC_002967:TDE0886|5end_hypothetical_protein_903341..903571_POSITIVE 250 166 121 210 160 NC_002967:TDE2189|5end_M23/M37_peptidase_domain_protein_2224148..2224378_NEGATIVE 249 99 52 212 165 NC_002967:TDE1026|5end_acyl_carrier_protein_1057302..1057532_POSITIVE 244 129 100 123 93 NC_002967:TDE0281|5end_hypothetical_protein_310490..310720_NEGATIVE 233 94 57 55 20 NC_002967:TDE0275|5end_CAAX_amino_terminal_protease_family_protein_306633..306863_POSITIVE 224 129 83 152 107 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 224 80 32 60 9 NC_002967:TDE1889|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_1910888..1911118_NEGATIVE 224 187 141 126 69 NC_002967:TDE0892|5end_ABC_transporter,_permease_protein_908571..908801_POSITIVE 223 201 162 113 72 NC_002967:TDE2371|5end_iron-sulfur_cluster-binding_protein_2403583..2403813_POSITIVE 220 173 150 53 26 NC_002967:TDE2678|5end_alpha-amylase_family_protein_2719390..2719620_NEGATIVE 219 192 151 164 116 NC_002967:TDE1599|5end_ABC_transporter,_ATP-binding/permease_protein_1650644..1650874_NEGATIVE 219 169 122 164 119 NC_002967:TDE0447|5end_TPR_domain_protein_502758..502988_POSITIVE 218 170 121 99 39 NC_002967:TDE0999|5end_formate/nitrite_transporter_1025870..1026100_POSITIVE 214 174 135 179 136 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 214 167 124 216 172 NC_002967:TDE0493|5end_hypothetical_protein_549342..549572_NEGATIVE 214 200 151 130 74 NC_002967:TDE0291|5end_hypothetical_protein_321060..321290_NEGATIVE 212 130 83 123 70 NC_002967:TDE1531|5end_hypothetical_protein_1575951..1576181_POSITIVE 212 205 171 119 84 NC_002967:TDE1475|5end_flagellar_filament_core_protein_1522191..1522421_NEGATIVE 209 188 145 228 183 NC_002967:TDE0018|5end_LysM_domain_protein_23573..23803_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 150 121 96 63 NC_002967:TDE0885|3end_50S_ribosomal_protein_L19_903384..903534_POSITIVE 240 168 121 69 13 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 224 187 141 67 10 NC_002967:TDE0891|3end_transcriptional_regulator,_putative_908592..908742_POSITIVE 223 201 162 57 16 NC_002967:TDE2370|3end_hypothetical_protein_2403607..2403757_POSITIVE 216 167 121 57 12 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 211 210 165 128 87 NC_002967:TDE1978|3end_hypothetical_protein_1991501..1991651_NEGATIVE 210 65 23 61 25 NC_002967:TDE1882|3end_glycosyl_hydrolase,_family_1_1904907..1905057_POSITIVE 209 188 145 136 91 NC_002967:TDE0019|3end_formate--tetrahydrofolate_ligase_23665..23815_NEGATIVE 204 196 152 68 22 NC_002967:TDE0686|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_723757..723907_POSITIVE 201 144 121 63 42 NC_002967:TDE2207|3end_hypothetical_protein_2245366..2245516_NEGATIVE 201 94 53 69 30 NC_002967:TDE0525|3end_hypothetical_protein_571163..571313_POSITIVE 199 177 136 71 23 NC_002967:TDE2683|3end_sigma_factor_WhiG_2723367..2723517_NEGATIVE 199 167 121 57 12 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 197 170 121 51 1 NC_002967:TDE2180|3end_tRNA_modification_GTPase_2210590..2210740_NEGATIVE 197 142 114 65 31 NC_002967:TDE1237|3end_hypothetical_protein_1270816..1270966_POSITIVE 196 139 103 50 16 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 196 165 121 126 84 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 196 187 148 146 102 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 196 166 129 139 102 NC_002967:TDE0009|3end_hypothetical_protein_13724..13874_NEGATIVE 195 229 183 126 65 NC_002967:TDE2296|3end_hypothetical_protein_2334283..2334433_NEGATIVE