Origin IGS: ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttaatttccttacttcaatttaatctttttttatcttttcaaataccgttatcaggccccagcctgcaagcatacagaggactgcaaccagcctcatcgaaggcagcag Mask Tandem Repeat Region ================================================ ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac Find is-nt database================================================ Query_seq: TDE2250:TDE2251|TDE2250:TDE2251:hypothetical protein:uracil permease:->->:2289470..2289579 110 ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2250:TDE2251|TDE2250:TDE2251:hypothetical protein:uracil permease:->->:2289470..2289579 110 ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2250:TDE2251|TDE2250:TDE2251:hypothetical protein:uracil permease:->->:2289470..2289579 110 ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 2 End: 106 . A A K S S A P Q L G R Y A Q L S P G S L P I Q F S L F L N F Q L L S M .... ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac 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================================================ ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2250:TDE2251|TDE2250:TDE2251:hypothetical protein:uracil permease:->->:2289470..2289579 110 ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE2250_TDE2251|hypothetical protein:uracil permease|POSITIVE:POSITIVE|[2289470,2289579]|110 HSP 1 e-value: 9.0E-44 bit: 176.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagatnnnnnnngattaaattgaagtaaggaaattaac ctgctgccttcgatgaggctggttgcagtcctctgtatgcttgcaggctggggcctgataacggtatttgaaaagataaaaaaagattaaattgaagtaaggaaattaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCUGCCUUCGAUGAGGCUGGUUGCAGUCCUCUGUAUGCUUGCAGGCUGGGGCCUGAUAACGGUAUUUGAAAAGAUAAAAAAAGAUUAAAUUGAAGUAAGGAAAUUAAC ...((..((((((((((((((....))).))))......(((.(((((....))))).......(((((....)))))....))).....)))))))..))......... (-26.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAAUUUCCUUACUUCAAUUUAAUCUUUUUUUAUCUUUUCAAAUACCGUUAUCAGGCCCCAGCCUGCAAGCAUACAGAGGACUGCAACCAGCCUCAUCGAAGGCAGCAG .............((((...............................(((..(((((....)))))..))).....((((.(((....)))))))...))))....... (-22.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 50 1 87 42 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 396 50 3 76 40 NC_002967:TDE1146|5end_hypothetical_protein_1185414..1185644_NEGATIVE 393 50 1 223 170 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 369 50 1 202 158 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 364 70 23 219 163 NC_002967:TDE2640|5end_hypothetical_protein_2680034..2680264_POSITIVE 362 69 25 78 46 NC_002967:TDE1912|5end_redox-sensing_transcriptional_repressor_Rex_1929176..1929406_POSITIVE 352 50 4 131 98 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 352 48 2 79 20 NC_002967:TDE2005|5end_hypothetical_protein_2023776..2024006_POSITIVE 352 47 1 202 151 NC_002967:TDE1664|5end_hypothetical_protein_1717862..1718092_POSITIVE 346 58 12 215 155 NC_002967:TDE2282|5end_tRNA_synthetase,_class_II_family_protein_2319665..2319895_NEGATIVE 346 55 16 62 25 NC_002967:TDE0425|5end_bacteriocin_ABC_transporter,_ATP-binding/permease,_putative_479700..479930_POSITIVE 339 50 6 183 140 NC_002967:TDE2069|5end_endoribonuclease_L-PSP,_putative_2096632..2096862_POSITIVE 336 57 14 83 23 NC_002967:TDE1405|5end_phosphoribosylformylglycinamidine_synthetase_I_1448674..1448904_NEGATIVE 335 35 1 142 104 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 335 53 11 149 116 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 333 57 11 135 93 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 333 60 11 162 102 NC_002967:TDE1233|5end_hypothetical_protein_1267203..1267433_POSITIVE 330 36 1 223 174 NC_002967:TDE2250|5end_hypothetical_protein_2288568..2288798_POSITIVE 330 49 3 86 23 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 330 56 14 50 8 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 50 1 77 20 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 365 50 3 145 94 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 364 57 11 53 2 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 358 49 1 151 108 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 357 50 6 140 95 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 352 48 2 68 9 NC_002967:TDE2004|3end_hypothetical_protein_2023845..2023995_POSITIVE 347 49 1 50 3 NC_002967:TDE2162|3end_NOL1/NOP2/sun_family_protein_2195560..2195710_POSITIVE 346 55 16 55 18 NC_002967:TDE0424|3end_bacteriocin-type_signal_domain_protein_479773..479923_POSITIVE 340 53 13 65 12 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 339 50 6 66 23 NC_002967:TDE2068|3end_antigen,_putative_2096595..2096745_POSITIVE 336 57 14 80 20 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE 335 35 1 140 102 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 335 53 11 81 48 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 330 56 14 53 11 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 322 54 14 77 33 NC_002967:TDE2738|3end_oligoendopeptidase_F,_putative_2794573..2794723_POSITIVE 320 53 13 88 35 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 319 49 8 63 15 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 317 57 20 54 11 NC_002967:TDE1859|3end_hypothetical_protein_1886230..1886380_POSITIVE 317 50 2 69 24 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 316 57 18 139 97 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE