Origin IGS: taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaactgtagccaaacaaggtggtcttgatcgattaaacgtcaagatcaccttgtttggctcctaatctgacacttgcgtagtagagtaagcctgcacgttgaaatcttgggctctctctgccggttccatcatgggagtgagctatcgttcatcgcctta Mask Tandem Repeat Region ================================================ taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta Find is-nt database================================================ Query_seq: TF3013:TF3014|TF3013:TF3014:conserved hypothetical protein:oxidoreductase, short-chain dehydrogenase/reductase family:->->:3237600..3237762 163 taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3013:TF3014|TF3013:TF3014:conserved hypothetical protein:oxidoreductase, short-chain dehydrogenase/reductase family:->->:3237600..3237762 163 taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3013:TF3014|TF3013:TF3014:conserved hypothetical protein:oxidoreductase, short-chain dehydrogenase/reductase family:->->:3237600..3237762 163 taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 15 End: 125 .............. M A H S H D G T G R E S P R F Q R A G L L Y Y A S V R L G A K Q G D L D V ...................................... taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta 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================================================ taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -22.7 Tail_Score: -2.63631 Start: 99 End: 155 Full_Region: taaaaact gtagccaaacaaggtggtcttgatcg attaaa cgtcaagatcaccttgtttggctcc taatctgacacttgc ..................................................................................................gtagccaaacaaggtggtcttgatcgattaaacgtcaagatcaccttgtttggctcc........ TransTerm Strand: + Conf: 81 HP_score: -11.2 Tail_Score: -3.67989 Start: 108 End: 146 Full_Region: AGATTAGGAGCCAAA CAAGGTGATCTTGACG TTTAAT CGATCAAGACCACCTTG TTTGGCTACAGTTTT ...........................................................................................................CAAGGTGATCTTGACGTTTAATCGATCAAGACCACCTTG................. TransTerm Strand: + Conf: 71 HP_score: -7.1 Tail_Score: -3.96483 Start: 111 End: 143 Full_Region: TTAGGAGCCAAACAA GGTGATCTTGACG TTTAAT CGATCAAGACCACC TTGTTTGGCTACAGT ..............................................................................................................GGTGATCTTGACGTTTAATCGATCAAGACCACC.................... Find igs database================================================ Query_seq: TF3013:TF3014|TF3013:TF3014:conserved hypothetical protein:oxidoreductase, short-chain dehydrogenase/reductase family:->->:3237600..3237762 163 taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: tfor_TF3013_TF3014|conserved hypothetical protein:oxidoreductase, short-chain dehydrogenase/reductase family|POSITIVE:POSITIVE|[3237600,3237762]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta taaggcgatgaacgatagctcactcccatgatggaaccggcagagagagcccaagatttcaacgtgcaggcttactctactacgcaagtgtcagattaggagccaaacaaggtgatcttgacgtttaatcgatcaagaccaccttgtttggctacagttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGCGAUGAACGAUAGCUCACUCCCAUGAUGGAACCGGCAGAGAGAGCCCAAGAUUUCAACGUGCAGGCUUACUCUACUACGCAAGUGUCAGAUUAGGAGCCAAACAAGGUGAUCUUGACGUUUAAUCGAUCAAGACCACCUUGUUUGGCUACAGUUUUUA ....(((.((((.....((((.(((...((.((....)).))))).)))).......)))).))).....((((.(((..(((....)))..))).)))).(((((((((((((.((((((((......)).)))))).)))))))))))))........... (-54.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAACUGUAGCCAAACAAGGUGGUCUUGAUCGAUUAAACGUCAAGAUCACCUUGUUUGGCUCCUAAUCUGACACUUGCGUAGUAGAGUAAGCCUGCACGUUGAAAUCUUGGGCUCUCUCUGCCGGUUCCAUCAUGGGAGUGAGCUAUCGUUCAUCGCCUUA ....(((((.(((((((((((((((((((((.((......)))))))))))))))))))))))....................((((((..(((((...............)))))..))))))))))).......((..((((((....))))))..))... (-61.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 50 3 136 93 tfor:TF3145|5end_conserved_hypothetical_protein;_possible_GTP_cyclohydrolase_I_family_3381254..3381484_POSITIVE 374 60 18 221 179 tfor:TF1064|5end_ampG_permease_1134004..1134234_POSITIVE 357 50 4 50 2 tfor:TF2771|5end_undecaprenol_kinase,_bacitracin_resistance_protein_2956559..2956789_POSITIVE 348 77 37 107 61 tfor:TF1257|5end_hypothetical_protein_1338118..1338348_POSITIVE 348 77 37 72 26 tfor:TF1256|5end_hypothetical_protein_1338083..1338313_POSITIVE 339 50 6 154 103 tfor:TF0561|5end_DNA_binding_protein;_possible__HU_protein_593548..593778_POSITIVE 331 68 22 131 80 tfor:TF0280|5end_hypothetical_protein_308807..309037_POSITIVE 323 50 6 196 143 tfor:TF1322|5end_conserved_hypothetical_protein;_possible_surface_protein_1401864..1402094_POSITIVE 322 53 11 200 160 tfor:TF0763|5end_chromate_transport_protein_809675..809905_POSITIVE 321 70 25 100 54 tfor:TF0259|5end_conserved_hypothetical_protein_289750..289980_POSITIVE 320 49 5 223 183 tfor:TF1733|5end_conserved_hypothetical_protein_1856015..1856245_POSITIVE 320 50 2 104 46 tfor:TF0394|5end_oxaloacetate_decarboxylase,_alpha_subunit_(pyruvate_carboxylase,_C-terminal_domain)_413268..413498_POSITIVE 318 69 23 192 146 tfor:TF2519|5end_membrane_protein,_metallopeptidase_M23/M37_family_2697676..2697906_POSITIVE 318 55 11 188 138 tfor:TF0925|5end_hypothetical_protein_961736..961966_POSITIVE 318 50 13 34 1 tfor:TF0231|5end_conserved_hypothetical_protein_257804..258034_POSITIVE 316 45 3 228 180 tfor:TF2022|5end_conserved_hypothetical_protein_2178524..2178754_POSITIVE 315 50 5 81 28 tfor:TF2791|5end_GTP-binding_protein_TypA_2975298..2975528_POSITIVE 315 53 13 171 134 tfor:TF0451|5end_rhomboid_family_membrane_protein_470085..470315_POSITIVE 313 50 4 203 162 tfor:TF2219|5end_two-component_system_sensor_histidine_2390844..2391074_POSITIVE 312 43 6 75 34 tfor:TF0520|5end_tetraacyldisaccharide_4'-kinase_544752..544982_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 49 3 139 82 tfor:TF2979|3end_possible_outer_membrane__protein_3193164..3193314_POSITIVE 357 50 4 50 2 tfor:TF2770|3end_conserved_hypothetical_protein_2956639..2956789_POSITIVE 348 77 37 60 14 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE 344 48 3 82 31 tfor:TF2657|3end_conserved_hypothetical_protein_2830873..2831023_POSITIVE 338 46 4 59 10 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 320 49 5 107 67 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE 318 69 23 147 101 tfor:TF2518|3end_ATP-dependent_DNA_helicase_2697711..2697861_POSITIVE 318 46 2 108 46 tfor:TF2179|3end_integral_membrane_protein,_MarC_family_2352369..2352519_POSITIVE 318 55 11 76 26 tfor:TF0923|3end_tetracycline_resistance_element_mobilization_regulatory_protein_961704..961854_POSITIVE 312 43 6 57 16 tfor:TF0519|3end_thiamine_monophosphate_kinase_544814..544964_POSITIVE 306 57 13 57 9 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 302 100 51 110 47 tfor:TF0598|3end_hypothetical_protein_629500..629650_POSITIVE 300 49 1 147 84 tfor:TF1390|3end_possible_transposase_1463906..1464056_POSITIVE 300 69 22 48 1 tfor:TF0404|3end_conserved_hypothetical_protein_423847..423997_POSITIVE 300 49 1 147 84 tfor:TF0198|3end_transposase_related_sequence_222066..222216_POSITIVE 298 54 13 83 37 tfor:TF1899|3end_anti-sigma_factor_2053815..2053965_POSITIVE 295 50 3 85 36 tfor:TF1581|3end_hypothetical_protein_1689467..1689617_POSITIVE 295 68 28 70 17 tfor:TF0696|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_740741..740891_POSITIVE 293 50 2 92 26 tfor:TF0624|3end_Xaa-Pro_dipeptidase_(aminopeptidase_P)_661015..661165_POSITIVE 292 66 28 39 2 tfor:TF0072|3end_hypothetical_protein_81070..81220_POSITIVE