Origin IGS: tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttataaaaaaatga .........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 tcatttttttataaatatactaaataaaatataccgtaaatcattataatttatacatgcttgaaaattattctcatcaattattcttaagttaatcatcgaatcttactatatattcaaaacacgtatttgtcaagacaaagttttatcgtccgcatgaaaacttaaagcacttcgcaagttgaacatacttaca Mask Tandem Repeat Region ================================================ tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttataaaaaaatga Find is-nt database================================================ Query_seq: TDE0900:TDE0901|TDE0900:TDE0901:ABC transporter, ATP-binding protein:hypothetical protein:-><-:918753..918948 196 tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttataaaaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0900:TDE0901|TDE0900:TDE0901:ABC transporter, ATP-binding protein:hypothetical protein:-><-:918753..918948 196 tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttataaaaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0900:TDE0901|TDE0900:TDE0901:ABC transporter, ATP-binding protein:hypothetical protein:-><-:918753..918948 196 tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttataaaaaaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttataaaaaaatga Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 98 End: 193 ................................................................................................. M I N L R I I D E N N F Q A C I N Y N D L R Y I L F S I F I K K * ... tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttataaaaaaatga 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: 88 Start: 60 End: 89 ...........................................................CTTGACAAATACGTGTTTTGAATATATAGT........................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttataaaaaaatga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0900:TDE0901|TDE0900:TDE0901:ABC transporter, ATP-binding protein:hypothetical protein:-><-:918753..918948 196 tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttataaaaaaatga Intra-Species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: NC_002967_TDE0900_TDE0901|ABC transporter, ATP-binding protein:hypothetical protein|POSITIVE:NEGATIVE|[918753,918948]|196 HSP 1 e-value: 1.0E-101 bit: 369.0 Len: 186 Query Start:1 Query End:186 Subject Strand: POSITIVE Subject Start: 1 Subject End: 186 tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttat.......... tgtaagtatgttcaacttgcgaagtgctttaagttttcatgcggacgataaaactttgtcttgacaaatacgtgttttgaatatatagtaagattcgatgattaacttaagaataattgatgagaataattttcaagcatgtataaattataatgatttacggtatattttatttagtatatttat.......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAAGUAUGUUCAACUUGCGAAGUGCUUUAAGUUUUCAUGCGGACGAUAAAACUUUGUCUUGACAAAUACGUGUUUUGAAUAUAUAGUAAGAUUCGAUGAUUAACUUAAGAAUAAUUGAUGAGAAUAAUUUUCAAGCAUGUAUAAAUUAUAAUGAUUUACGGUAUAUUUUAUUUAGUAUAUUUAU .((((((.......))))))...(((((.((((((.(((...((((((.......)))))))))...((((((((((.(((.............(((((.(((........))).)))))...........)))))))))))))..........)))))).))))).................... (-29.15) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAUAUACUAAAUAAAAUAUACCGUAAAUCAUUAUAAUUUAUACAUGCUUGAAAAUUAUUCUCAUCAAUUAUUCUUAAGUUAAUCAUCGAAUCUUACUAUAUAUUCAAAACACGUAUUUGUCAAGACAAAGUUUUAUCGUCCGCAUGAAAACUUAAAGCACUUCGCAAGUUGAACAUACUUACA .........................((((......(((((((...((....)).))))))).....((((((....(((((((..((((.((((.(......).)))).....(((..(((((....))))).......)))....)))).))))))).((.....)).))))))......)))). (-15.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 97 55 180 137 NC_002967:TDE1280|5end_hypothetical_protein_1316451..1316681_NEGATIVE 247 67 22 211 156 NC_002967:TDE1239|5end_hypothetical_protein_1271363..1271593_NEGATIVE 239 90 48 197 155 NC_002967:TDE1898|5end_translocase_1920890..1921120_NEGATIVE 238 58 12 150 104 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 237 45 3 182 132 NC_002967:TDE1682|5end_V-type_ATP_synthase_subunit_B_1734843..1735073_NEGATIVE 235 50 1 184 118 NC_002967:TDE0463|5end_purine_nucleoside_phosphorylase_517183..517413_POSITIVE 234 50 9 71 22 NC_002967:TDE0769|5end_ribosomal_protein_L23_807634..807864_POSITIVE 231 50 4 191 146 NC_002967:TDE2403|5end_metallo-beta-lactamase_family_protein_2429282..2429512_NEGATIVE 231 159 111 79 31 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 230 90 41 189 140 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 229 45 1 169 119 NC_002967:TDE0171|5end_nuclease_SbcCD,_C_subunit,_putative_199965..200195_POSITIVE 224 58 19 211 178 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 224 49 1 216 173 NC_002967:TDE0462|5end_metallo-beta-lactamase_family_protein_516987..517217_NEGATIVE 224 45 1 66 6 NC_002967:TDE0165|5end_hypothetical_protein_194122..194352_POSITIVE 223 54 16 171 136 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 223 66 23 90 47 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 222 65 36 162 134 NC_002967:TDE2255|5end_hypothetical_protein_2291591..2291821_POSITIVE 222 97 55 200 142 NC_002967:TDE1046|5end_hypothetical_protein_1073646..1073876_POSITIVE 221 57 17 86 48 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 221 66 24 150 107 NC_002967:TDE1005|5end_hypothetical_protein_1030206..1030436_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 45 1 148 106 NC_002967:TDE1140|3end_hypothetical_protein_1168730..1168880_NEGATIVE 251 48 13 82 44 NC_002967:TDE2292|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_2329383..2329533_POSITIVE 248 79 32 81 36 NC_002967:TDE0108|3end_hypothetical_protein_128787..128937_POSITIVE 239 90 48 145 103 NC_002967:TDE1899|3end_hypothetical_protein_1920942..1921092_NEGATIVE 239 48 15 143 109 NC_002967:TDE1494|3end_chemotaxis_protein_CheY_1539596..1539746_POSITIVE 234 50 9 68 19 NC_002967:TDE0768|3end_50S_ribosomal_protein_L4_807711..807861_POSITIVE 232 44 8 134 94 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 229 45 1 144 94 NC_002967:TDE0170|3end_nuclease_SbcCD,_D_subunit,_putative_200020..200170_POSITIVE 229 60 15 57 15 NC_002967:TDE0095|3end_hypothetical_protein_112622..112772_POSITIVE 224 179 141 42 5 NC_002967:TDE2469|3end_hexokinase_family_protein_2491236..2491386_NEGATIVE 223 50 11 151 109 NC_002967:TDE1347|3end_hypothetical_protein_1388032..1388182_POSITIVE 221 63 21 122 85 NC_002967:TDE2318|3end_LysM_domain/M23/M37_peptidase_domain_protein_2355868..2356018_POSITIVE 220 45 9 135 92 NC_002967:TDE1309|3end_modulator_of_DNA_gyrase_family_protein_1346042..1346192_POSITIVE 215 57 20 151 121 NC_002967:TDE1960|3end_hypothetical_protein_1974569..1974719_POSITIVE 212 45 13 150 117 NC_002967:TDE0392|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_441846..441996_NEGATIVE 210 59 11 78 25 NC_002967:TDE0830|3end_hypothetical_protein_851609..851759_NEGATIVE 209 50 19 75 46 NC_002967:TDE2130|3end_hypothetical_protein_2161574..2161724_NEGATIVE 208 48 7 110 73 NC_002967:TDE0823|3end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_845252..845402_POSITIVE 207 44 13 134 102 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 206 59 20 64 21 NC_002967:TDE1286|3end_TPR_domain_protein_1322817..1322967_POSITIVE