Origin IGS: tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtcattttaatttgtattacttttgtaataaataaaataattcccccccttccccaaaaaagccaaccgttgcctgatcaaggcagcggttggtcatcaatca Mask Tandem Repeat Region ================================================ tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac Find is-nt database================================================ Query_seq: TF1362:TF1363|TF1362:TF1363:hypothetical protein:conserved hypothetical protein:->->:1444120..1444222 103 tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1362:TF1363|TF1362:TF1363:hypothetical protein:conserved hypothetical protein:->->:1444120..1444222 103 tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1362:TF1363|TF1362:TF1363:hypothetical protein:conserved hypothetical protein:->->:1444120..1444222 103 tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 2 End: 100 . I S S W G S G Q D P L P Q S K Q P L P P I I K N I V F T I C I L M ... tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac 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: 81 Start: 71 End: 100 ......................................................................ATTTATTACAAAAGTAATACAAATTAAAAT... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1362:TF1363|TF1362:TF1363:hypothetical protein:conserved hypothetical protein:->->:1444120..1444222 103 tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: tfor_TF1362_TF1363|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1444120,1444222]|103 HSP 1 e-value: 1.0E-39 bit: 163.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaannnnnnnaattattttatttattacaaaagtaatacaaattaaaatgac tgattgatgaccaaccgctgccttgatcaggcaacggttggcttttttggggaagggggggaattattttatttattacaaaagtaatacaaattaaaatgac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUGAUGACCAACCGCUGCCUUGAUCAGGCAACGGUUGGCUUUUUUGGGGAAGGGGGGGAAUUAUUUUAUUUAUUACAAAAGUAAUACAAAUUAAAAUGAC ..........(((((((.(((((.....))))).)))))))(((((((.....)))))))...((((((((..((((((....)))))).....)))))))). (-26.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCAUUUUAAUUUGUAUUACUUUUGUAAUAAAUAAAAUAAUUCCCCCCCUUCCCCAAAAAAGCCAACCGUUGCCUGAUCAAGGCAGCGGUUGGUCAUCAAUCA ...((((((.....((((((....))))))..)))))).......................((((((((((((((.....))))))))))))))......... (-31.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 58 11 57 1 tfor:TF2747|5end_heat_shock_protein,_HSP90_family_2928279..2928509_POSITIVE 418 60 14 223 181 tfor:TF2208|5end_conserved_hypothetical_protein_2382349..2382579_POSITIVE 407 60 11 203 138 tfor:TF1900|5end_conserved_hypothetical_protein_2053867..2054097_POSITIVE 379 60 14 198 150 tfor:TF2849|5end_histidinol-phosphate_transaminase_3037288..3037518_POSITIVE 369 58 17 219 180 tfor:TF0419|5end_conserved_hypothetical_protein_435250..435480_POSITIVE 365 58 17 187 134 tfor:TF0992|5end_hypothetical_protein_1048251..1048481_POSITIVE 364 58 21 188 147 tfor:TF1036|5end_iron(III)_ABC_transporter,_permease_component_1097160..1097390_POSITIVE 359 59 11 200 145 tfor:TF2922|5end_surface_antigen_BspA_3119122..3119352_POSITIVE 359 57 12 71 26 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 357 47 1 169 121 tfor:TF2253|5end_conjugative_transposon_protein,_TraG_2424950..2425180_POSITIVE 354 50 1 206 158 tfor:TF3072|5end_conserved_hypothetical_protein_3295302..3295532_POSITIVE 348 59 16 52 15 tfor:TF1624|5end_carboxyl-terminal_protease_1737252..1737482_POSITIVE 345 60 14 128 85 tfor:TF2204|5end_conserved_hypothetical_protein_2378866..2379096_POSITIVE 343 51 11 76 36 tfor:TF1315|5end_purine_nucleoside_phosphorylase_1390236..1390466_POSITIVE 340 60 11 63 18 tfor:TF0974|5end_hypothetical_protein_1024189..1024419_POSITIVE 336 60 11 110 47 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 335 60 11 224 167 tfor:TF2245|5end_conserved_hypothetical_protein_2420654..2420884_POSITIVE 334 60 15 78 34 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 333 42 5 76 34 tfor:TF2512|5end_possible_abortive_infection_protein_2690247..2690477_POSITIVE 331 56 15 72 17 tfor:TF1910|5end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase_2064001..2064231_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 41 11 80 50 tfor:TF1362|3end_hypothetical_protein_1444059..1444209_POSITIVE 407 60 11 71 6 tfor:TF1899|3end_anti-sigma_factor_2053815..2053965_POSITIVE 348 59 16 52 15 tfor:TF1623|3end_5-formyltetrahydrofolate_cyclo-ligase_1737332..1737482_POSITIVE 344 57 16 101 72 tfor:TF0880|3end_conserved_hypothetical_protein_934371..934521_POSITIVE 343 51 11 62 22 tfor:TF1314|3end_conserved_hypothetical_protein_1390302..1390452_POSITIVE 335 60 15 137 98 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 331 56 15 66 11 tfor:TF1909|3end_cobalamin_(5`-phosphate)_synthase_2064075..2064225_POSITIVE 327 59 11 135 92 tfor:TF1867|3end_transposase_2023612..2023762_POSITIVE 327 59 11 129 70 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 326 59 14 143 90 tfor:TF1885|3end_conserved_hypothetical_protein_2038751..2038901_POSITIVE 320 53 16 68 42 tfor:TF1852|3end_prtQ_protein_2006546..2006696_POSITIVE 315 65 27 64 32 tfor:TF1001|3end_penicillin-binding_protein_1A_1056600..1056750_POSITIVE 314 58 15 137 94 tfor:TF2184|3end_conserved_hypothetical_protein_2357043..2357193_POSITIVE 314 57 16 112 64 tfor:TF1943|3end_phosphoenolpyruvate_carboxykinase_2092465..2092615_POSITIVE 312 50 1 151 98 tfor:TF0228|3end_probable_integral_outer_membrane_protein_254809..254959_POSITIVE 311 49 3 133 90 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 310 69 23 142 84 tfor:TF1306|3end_hypothetical_protein_1387062..1387212_POSITIVE 310 50 6 78 34 tfor:TF0239|3end_conserved_hypothetical_protein_270323..270473_POSITIVE 308 50 10 148 104 tfor:TF2945|3end_DNA-directed_RNA_polymerase_beta'_subunit_3151802..3151952_POSITIVE 305 60 17 52 8 tfor:TF1597|3end_TatD_family_protein_1713418..1713568_POSITIVE