Origin IGS: taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatgatacgcaaacctatgcgtaaaagtgcggtgcattatagcggagtttcttaaccttgccaaaataatccgaagcatgatgtgcgttatgattcaagtgtcaacagtaagcgctaaatcatacactcatcacaaaaccctta Mask Tandem Repeat Region ================================================ taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt Find is-nt database================================================ Query_seq: AA00634:AA00635|AA00634:AA00635:DNA polymerase IV (Pol IV):dihydropteroate synthase:->->:435892..436036 145 taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00634:AA00635|AA00634:AA00635:DNA polymerase IV (Pol IV):dihydropteroate synthase:->->:435892..436036 145 taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00634:AA00635|AA00634:AA00635:DNA polymerase IV (Pol IV):dihydropteroate synthase:->->:435892..436036 145 taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 51 End: 143 .................................................. M I T H I M L R I I L A R L R N S A I M H R T F T H R F A Y H .. Protein_Len: 39 Strand: - Start: 2 End: 118 . L T K H H T Y S K A S V T S V Q I M V C M M S R I I K A L N L F E A I I C R M ........................... taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt 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: 87 Start: 80 End: 109 ...............................................................................TTTGGCAAGGTTAAGAAACTCCGCTATAAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00634:AA00635|AA00634:AA00635:DNA polymerase IV (Pol IV):dihydropteroate synthase:->->:435892..436036 145 taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: aact_AA00634_AA00635|DNA polymerase IV (Pol IV):dihydropteroate synthase|POSITIVE:POSITIVE|[435892,436036]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt taagggttttgtgatgagtgtatgatttagcgcttactgttgacacttgaatcataacgcacatcatgcttcggattattttggcaaggttaagaaactccgctataatgcaccgcacttttacgcataggtttgcgtatcattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGGUUUUGUGAUGAGUGUAUGAUUUAGCGCUUACUGUUGACACUUGAAUCAUAACGCACAUCAUGCUUCGGAUUAUUUUGGCAAGGUUAAGAAACUCCGCUAUAAUGCACCGCACUUUUACGCAUAGGUUUGCGUAUCAUUU .((((.....((((((.(((((((((((((.((........).).).)))))))).)))).))))))....(((..((((.((((..((((....))))..)))).))))..)))..))))((((((......))))))...... (-35.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGAUACGCAAACCUAUGCGUAAAAGUGCGGUGCAUUAUAGCGGAGUUUCUUAACCUUGCCAAAAUAAUCCGAAGCAUGAUGUGCGUUAUGAUUCAAGUGUCAACAGUAAGCGCUAAAUCAUACACUCAUCACAAAACCCUUA ......((((((......))))))...((((..((.(((((.(((..(((....)))..)))....))))).))..))))((((.(.((.((((((..(((((.........))))).)))))))).).))))............ (-31.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 126 82 78 35 aact:AA01303|5end_competence_protein_A_881996..882226_POSITIVE 385 127 81 56 8 aact:AA02846|5end_crossover_junction_endodeoxyribonuclease_1998648..1998878_POSITIVE 364 122 87 179 143 aact:AA00190|5end_triosephosphate_isomerase_134088..134318_POSITIVE 354 138 91 52 8 aact:AA01660|5end_hypothetical_protein_1125035..1125265_POSITIVE 346 120 71 120 69 aact:AA01291|5end_excinuclease_ABC_subunit_A_872829..873059_POSITIVE 329 120 73 108 61 aact:AA01008|5end_mazG_beta-lactamase_regulatory_protein_homolog_703470..703700_POSITIVE 328 128 90 180 143 aact:AA01992|5end_protease_IV;_signal_peptide_peptidase;_Endopeptidase_IV_1353029..1353259_POSITIVE 325 126 83 44 2 aact:AA01041|5end_hypothetical_protein_724853..725083_POSITIVE 324 136 97 138 100 aact:AA00988|5end_conserved_hypothetical_protein_690898..691128_POSITIVE 323 120 72 111 64 aact:AA00160|5end_pilA-like_biogenesis_protein_/_prepilin_peptidase_dependent_proteinD_112836..113066_POSITIVE 320 122 83 123 80 aact:AA01603|5end_oligopeptidase_A_1082898..1083128_POSITIVE 319 90 41 62 10 aact:AA02250|5end_possible_cytochrome_c-type_protein_1530125..1530355_POSITIVE 317 130 84 137 88 aact:AA00134|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_(menaquinone_biosynthetic_protein)_95317..95547_POSITIVE 312 125 83 187 142 aact:AA01522|5end_conserved_hypothetical_protein_1022840..1023070_POSITIVE 310 137 93 148 108 aact:AA01027|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_717676..717906_POSITIVE 309 136 97 193 152 aact:AA02972|5end_conserved_hypothetical_protein_(tyrosine_phenol_lyase-related_protein)_2077381..2077611_POSITIVE 309 74 32 53 8 aact:AA00113|5end_uracil_phosphoribosyltransferase_81286..81516_POSITIVE 305 123 84 141 102 aact:AA01694|5end_PTS_system,_IIA_component_1149929..1150159_POSITIVE 304 125 82 187 143 aact:AA00679|5end_cytoplasmic_axial_filament_(Ribonuclease_G)_463288..463518_POSITIVE 303 137 91 157 110 aact:AA01416|5end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_952780..953010_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 126 82 97 54 aact:AA01301|3end_competence_protein_B_882095..882245_POSITIVE 364 122 87 64 28 aact:AA00189|3end_dihydroxynaphthoic_acid_synthase_(naphthoate_synthas)_134053..134203_POSITIVE 346 120 71 59 8 aact:AA01289|3end_hypothetical_protein_872848..872998_POSITIVE 343 120 79 88 47 aact:AA00574|3end_regulatory_protein_392381..392531_POSITIVE 328 128 90 74 37 aact:AA01991|3end_conserved_hypothetical_protein_(possible_nitroreductase)_1353003..1353153_POSITIVE 327 120 71 66 7 aact:AA01224|3end_CTP_synthase_837899..838049_POSITIVE 325 126 83 57 15 aact:AA01040|3end_possible_lipoprotein_724946..725096_POSITIVE 323 120 72 130 83 aact:AA00158|3end_ampD_signalling_protein_(N-acetylmuramyl-L-alanine_amidase)_112935..113085_POSITIVE 309 136 97 123 82 aact:AA02970|3end_tyrosine_phenol-lyase_2077391..2077541_POSITIVE 305 123 84 61 22 aact:AA01692|3end_hexulose-6-phosphate_synthase_1149929..1150079_POSITIVE 304 125 82 67 23 aact:AA00675|3end_glutaredoxin_2_463248..463398_POSITIVE 303 120 74 74 33 aact:AA01954|3end_excinuclease_ABC,_subunit_C_1322314..1322464_POSITIVE 303 136 100 43 9 aact:AA00973|3end_transcriptional_regulator,_DeoR_family_679237..679387_POSITIVE 299 126 81 106 61 aact:AA02307|3end_5'-guanylate_kinase_1578058..1578208_POSITIVE 297 127 82 85 42 aact:AA00882|3end_hypothetical_protein_613645..613795_POSITIVE 296 137 93 95 51 aact:AA00578|3end_DNA_topoisomerase_395201..395351_POSITIVE 294 123 83 151 109 aact:AA01520|3end_hypothetical_protein_1022887..1023037_POSITIVE 292 137 93 65 19 aact:AA02142|3end_outer_membrane_protein_OprM_precursor_1467532..1467682_POSITIVE 291 138 99 112 68 aact:AA00167|3end_possible_amino-acid_transporter_(sodium-alanine_symporters)_119689..119839_POSITIVE 288 137 91 74 30 aact:AA01517|3end_peptidyl-prolyl_cis-trans_isomerase;_macrophage_infectivity_protein_1021791..1021941_POSITIVE