Origin IGS: tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatgtaagactattctaacatatgattaaaaatcggtcaagggtaaaatttgaaatttgaaaaaaatctgattttttttgtatgaattactgtagtagtattgataagtgcggctatttcggttaaaataaaaatagcttttatgggagtttaaa Mask Tandem Repeat Region ================================================ tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat Find is-nt database================================================ Query_seq: TDE2520:TDE2521|TDE2520:TDE2521:hypothetical protein:hypothetical protein:<-<-:2547889..2548044 156 tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2520:TDE2521|TDE2520:TDE2521:hypothetical protein:hypothetical protein:<-<-:2547889..2548044 156 tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2520:TDE2521|TDE2520:TDE2521:hypothetical protein:hypothetical protein:<-<-:2547889..2548044 156 tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 12 End: 116 ........... M K A I F I L T E I A A L I N T T T V I H T K K I R F F S N F K F Y P ........................................ tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat 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: 91 Start: 27 End: 56 ..........................ATTGATAAGTGCGGCTATTTCGGTTAAAAT.................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 89 Start: 115 End: 144 ..................................................................................................................CTTGACCGATTTTTAATCATATGTTAGAAT............ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2520:TDE2521|TDE2520:TDE2521:hypothetical protein:hypothetical protein:<-<-:2547889..2548044 156 tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_002967_TDE2520_TDE2521|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2547889,2548044]|156 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacnnnnnnnntcagannnnnnncaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat tttaaactcccataaaagctatttttattttaaccgaaatagccgcacttatcaatactactacagtaattcatacaaaaaaaatcagatttttttcaaatttcaaattttacccttgaccgatttttaatcatatgttagaatagtcttacatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAACUCCCAUAAAAGCUAUUUUUAUUUUAACCGAAAUAGCCGCACUUAUCAAUACUACUACAGUAAUUCAUACAAAAAAAAUCAGAUUUUUUUCAAAUUUCAAAUUUUACCCUUGACCGAUUUUUAAUCAUAUGUUAGAAUAGUCUUACAUAU .................((((((((..........))))))))............((((.....))))...........(((((((.((......)).....((((.........))))..)))))))....((((((.(((....))).)))))) (-16.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUGUAAGACUAUUCUAACAUAUGAUUAAAAAUCGGUCAAGGGUAAAAUUUGAAAUUUGAAAAAAAUCUGAUUUUUUUUGUAUGAAUUACUGUAGUAGUAUUGAUAAGUGCGGCUAUUUCGGUUAAAAUAAAAAUAGCUUUUAUGGGAGUUUAAA .......(((((.......((((..(..((((((((((((((.......)))))..(((....)))..))))))))).)..)))).....((((((..(((((....))))).(((((((..((....))..)))))))..)))))).)))))... (-26.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 80 31 171 122 NC_002967:TDE2520|5end_hypothetical_protein_2547798..2548028_NEGATIVE 686 90 41 179 130 NC_002967:TDE1829|5end_hypothetical_protein_1863647..1863877_NEGATIVE 255 50 3 147 95 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 248 49 7 129 85 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 231 68 34 83 44 NC_002967:TDE2543|5end_hypothetical_protein_2570950..2571180_NEGATIVE 231 68 34 207 168 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 228 50 7 185 133 NC_002967:TDE2569|5end_3-deoxy-7-phosphoheptulonate_synthase_2596308..2596538_POSITIVE 227 150 113 212 176 NC_002967:TDE1304|5end_hypothetical_protein_1339716..1339946_POSITIVE 226 50 10 127 88 NC_002967:TDE0783|5end_ribosomal_protein_L18_813520..813750_POSITIVE 225 80 35 174 129 NC_002967:TDE0241|5end_hypothetical_protein_275303..275533_NEGATIVE 224 77 42 94 59 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 220 128 82 115 64 NC_002967:TDE1897|5end_phosphoribosylglycinamide_formyltransferase_1918109..1918339_NEGATIVE 213 57 11 53 4 NC_002967:TDE2395|5end_Jag_protein,_putative_2423454..2423684_NEGATIVE 212 71 32 71 40 NC_002967:TDE0351|5end_L-lactate_dehydrogenase_395998..396228_NEGATIVE 207 140 91 191 151 NC_002967:TDE0699|5end_hypothetical_protein_735252..735482_NEGATIVE 205 66 21 152 99 NC_002967:TDE0786|5end_ribosomal_protein_L15_814602..814832_POSITIVE 203 45 7 227 195 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 203 45 7 126 94 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 200 68 21 141 90 NC_002967:TDE2043|5end_signal_recognition_particle-docking_protein_FtsY_2073058..2073288_NEGATIVE 199 60 15 191 137 NC_002967:TDE2721|5end_helicase_domain_protein_2779605..2779835_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 50 3 61 9 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 248 45 8 113 78 NC_002967:TDE2081|3end_hypothetical_protein_2112529..2112679_POSITIVE 248 49 7 116 72 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 239 66 28 73 37 NC_002967:TDE0680|3end_protein-export_membrane_protein_SecF_717613..717763_NEGATIVE 232 129 83 146 100 NC_002967:TDE0162|3end_hypothetical_protein_192882..193032_POSITIVE 231 68 34 98 59 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 226 50 10 116 77 NC_002967:TDE0782|3end_50S_ribosomal_protein_L6_813589..813739_POSITIVE 220 128 82 102 51 NC_002967:TDE1898|3end_translocase_1918122..1918272_NEGATIVE 220 67 34 105 73 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 209 65 34 50 11 NC_002967:TDE1251|3end_batB_protein,_putative_1286496..1286646_POSITIVE 207 140 91 112 72 NC_002967:TDE0700|3end_hypothetical_protein_735331..735481_NEGATIVE 203 45 7 106 74 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 200 68 21 151 100 NC_002967:TDE2044|3end_lipoprotein,_putative_2073048..2073198_NEGATIVE 199 60 15 130 76 NC_002967:TDE2722|3end_carhohydrate_kinase,_FGGY_family_2779666..2779816_NEGATIVE 198 55 22 147 111 NC_002967:TDE1690|3end_hypothetical_protein_1746583..1746733_NEGATIVE 195 49 6 95 46 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 195 68 21 151 99 NC_002967:TDE0785|3end_ribosomal_protein_L30_814682..814832_POSITIVE 194 47 17 123 93 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 192 59 16 124 88 NC_002967:TDE0008|3end_copper-translocating_P-type_ATPase_13646..13796_POSITIVE 190 69 24 72 1 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE