Origin IGS: taataaaaaaacacccgtaaaaaccaccgcactttaaactacaaaaggtttagcaaaaactaaaccttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggaacacctttactgataaattaaaataaaatgggttgttaaattaaatgtggcgcgattatagcacaacaatgtggcgggcagttagttcggcataacgtataaaaaacaaaaggtttagtttttgctaaaccttttgtagtttaaagtgcggtggtttttacgggtgtttttttatta Mask Tandem Repeat Region ================================================ taataaaaaaacacccgtaaaaaccaccgcactttaaactacaaaaggtttagcaaaaactaaaccttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc Find is-nt database================================================ Query_seq: AA02747:AA02748|AA02747:AA02748:ribose-phosphate pyrophosphokinase; phosphoribosylpyrophosphate synthase:conserved hypothetical protein:->->:1925319..1925498 180 taataaaaaaacacccgtaaaaaccaccgcactttaaactacaaaaggtttagcaaaaactaaaccttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02747:AA02748|AA02747:AA02748:ribose-phosphate pyrophosphokinase; phosphoribosylpyrophosphate synthase:conserved hypothetical protein:->->:1925319..1925498 180 taataaaaaaacacccgtaaaaaccaccgcactttaaactacaaaaggtttagcaaaaactaaaccttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02747:AA02748|AA02747:AA02748:ribose-phosphate pyrophosphokinase; phosphoribosylpyrophosphate synthase:conserved hypothetical protein:->->:1925319..1925498 180 taataaaaaaacacccgtaaaaaccaccgcactttaaactacaaaaggtttagcaaaaactaaaccttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataaaaaaacacccgtaaaaaccaccgcactttaaactacaaaaggtttagcaaaaactaaaccttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc Predict ORF larger than 30AA ================================================ taataaaaaaacacccgtaaaaaccaccgcactttaaactacaaaaggtttagcaaaaactaaaccttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc 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================================================ PromScan Matrix: RpoN Strand: - Score: 82 Start: 115 End: 131 ..................................................................................................................GTGGCGCGATTATAGCA................................................. taataaaaaaacacccgtaaaaaccaccgcactttaaactacaaaaggtttagcaaaaactaaaccttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.4 Tail_Score: -5.3236 Start: 42 End: 71 Full_Region: CCGCACTTTAAACTA CAAAAGGTTTAG CAAAAA CTAAACCTTTTG TTTTTTATACGTTAT .........................................CAAAAGGTTTAGCAAAAACTAAACCTTTTG............................................................................................................. TransTerm Strand: - Conf: 87 HP_score: -13.1 Tail_Score: -2.92613 Start: 42 End: 71 Full_Region: ataacgtataaaaaa caaaaggtttagt tttt gctaaaccttttg tagtttaaagtgcgg .........................................caaaaggtttagtttttgctaaaccttttg............................................................................................................. TransTerm Strand: + Conf: 87 HP_score: -6.5 Tail_Score: -5.49579 Start: 47 End: 66 Full_Region: CTTTAAACTACAAAA GGTTTAG CAAAAA CTAAACC TTTTGTTTTTTATAC ..............................................GGTTTAGCAAAAACTAAACC.................................................................................................................. TransTerm Strand: - Conf: 80 HP_score: -7.2 Tail_Score: -4.61566 Start: 47 End: 66 Full_Region: gtataaaaaacaaaa ggtttagt tttt gctaaacc ttttgtagtttaaag ..............................................ggtttagtttttgctaaacc.................................................................................................................. Find igs database================================================ Query_seq: AA02747:AA02748|AA02747:AA02748:ribose-phosphate pyrophosphokinase; phosphoribosylpyrophosphate synthase:conserved hypothetical protein:->->:1925319..1925498 180 taataaaaaaacacccgtaaaaaccaccgcactttaaactacaaaaggtttagcaaaaactaaaccttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc Intra-Species Hit: Count: 1 Min: 67 Max: 180 Len: 114 Subject: aact_AA02747_AA02748|ribose-phosphate pyrophosphokinase; phosphoribosylpyrophosphate synthase:conserved hypothetical protein|POSITIVE:POSITIVE|[1925319,1925498]|180 HSP 1 e-value: 2.0E-58 bit: 226.0 Len: 114 Query Start:67 Query End:180 Subject Strand: POSITIVE Subject Start: 67 Subject End: 180 ..................................................................ttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc ..................................................................ttttgttttttatacgttatgccgaactaactgcccgccacattgttgtgctataatcgcgccacatttaatttaacaacccattttattttaatttatcagtaaaggtgttcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGUUUUUUAUACGUUAUGCCGAACUAACUGCCCGCCACAUUGUUGUGCUAUAAUCGCGCCACAUUUAAUUUAACAACCCAUUUUAUUUUAAUUUAUCAGUAAAGGUGUUCC ...............((((........))))....((((....(((.((((.......)))).))).((((..(((.........)))..))))............)))).... (-10.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAACACCUUUACUGAUAAAUUAAAAUAAAAUGGGUUGUUAAAUUAAAUGUGGCGCGAUUAUAGCACAACAAUGUGGCGGGCAGUUAGUUCGGCAUAACGUAUAAAAAACAAAA ..(((((((.......................))).))))........(((.(.((.......)).).))).((((.(((((.....))))).))))................. (-16.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 67 33 161 124 aact:AA02230|5end_sugar_kinase_1515984..1516214_POSITIVE 336 60 20 41 1 aact:AA01589|5end_conserved_hypothetical_protein_1070300..1070530_POSITIVE 334 65 21 107 67 aact:AA00989|5end_hypothetical_protein_692319..692549_POSITIVE 328 66 22 143 94 aact:AA01335|5end_primosomal_protein_N'_901993..902223_POSITIVE 326 67 31 96 65 aact:AA02076|5end_conserved_hypothetical_protein_1409926..1410156_POSITIVE 326 63 30 162 126 aact:AA00993|5end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694488..694718_POSITIVE 326 69 21 191 140 aact:AA00796|5end_iron(III)_dicitrate_transport_system_permease_protein_545686..545916_POSITIVE 320 64 21 66 29 aact:AA00452|5end_phosphomannomutase;_phosphoglucomutase_315288..315518_POSITIVE 318 69 22 84 31 aact:AA01270|5end_hydrolase_(possible_2-haloalkanoic_acid_dehalogenase_I)_863317..863547_POSITIVE 318 60 14 225 176 aact:AA01166|5end_sulphite_synthesis_pathway_protein_798599..798829_POSITIVE 314 49 4 96 43 aact:AA00164|5end_dephospho-CoA_kinase_(dephosphocoenzyme_A_kinase)_116745..116975_POSITIVE 306 66 21 139 89 aact:AA02303|5end_ATP-dependent_DNA_helicase_1572696..1572926_POSITIVE 306 60 14 164 116 aact:AA01417|5end_probable_4-diphosphocytidyl-2C-methyl-D-erthyritol_synthase_(MEP_cytidyltransferase)_(MCT)_953256..953486_POSITIVE 305 63 31 216 180 aact:AA01477|5end_type_I_restriction_enzyme_R_protein_992249..992479_POSITIVE 305 52 18 127 91 aact:AA00329|5end_molybdopterin-guanine_dinucleotide_biosynthesis_protein_222737..222967_POSITIVE 304 65 21 201 162 aact:AA02052|5end_probable_exodeoxyribonuclease_VII_small_subunit_1398461..1398691_POSITIVE 304 63 21 79 23 aact:AA00652|5end_arginyl-tRNA_synthetase_(arginine--tRNA_ligase)_445718..445948_POSITIVE 301 62 31 216 188 aact:AA01107|5end_adenylosuccinate_lyase_762310..762540_POSITIVE 301 62 21 188 148 aact:AA00838|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_577522..577752_POSITIVE 301 64 21 196 141 aact:AA00790|5end_recombination_DNA_repair_protein_542455..542685_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 67 33 108 71 aact:AA02228|3end_regulatory_protein,_sorC_family_1516011..1516161_POSITIVE 336 60 20 41 1 aact:AA01588|3end_N-acetylmuramoyl-L-alanine_amidase_II_1070380..1070530_POSITIVE 326 67 31 69 38 aact:AA02075|3end_conserved_hypothetical_protein_1409979..1410129_POSITIVE 320 64 21 46 9 aact:AA00451|3end_hypothetical_protein_315348..315498_POSITIVE 318 69 22 100 47 aact:AA01269|3end_hypothetical_protein_863413..863563_POSITIVE 305 63 31 148 112 aact:AA01476|3end_hypothetical_protein_992261..992411_POSITIVE 300 60 20 52 17 aact:AA00937|3end_L-xylulokinase_647525..647675_POSITIVE 300 58 20 76 42 aact:AA00538|3end_hypothetical_protein_369111..369261_POSITIVE 299 59 15 57 14 aact:AA01753|3end_conserved_hypothetical_protein_1185902..1186052_POSITIVE 295 63 23 144 103 aact:AA02175|3end_anthranilate_synthase_component_II_1488966..1489116_POSITIVE 292 63 23 150 114 aact:AA00796|3end_iron(III)_dicitrate_transport_system_permease_protein_546752..546902_POSITIVE 290 59 20 53 19 aact:AA02965|3end_hypothetical_protein_2074286..2074436_POSITIVE 287 64 24 100 58 aact:AA02260|3end_pseudouridylate_synthase_I_1537962..1538112_POSITIVE 287 70 21 68 21 aact:AA01873|3end_mannose-6-phosphate_isomerase_1261940..1262090_POSITIVE 286 59 15 96 54 aact:AA00573|3end_chloramphenicol-sensitive_protein_RarD_393295..393445_POSITIVE 285 45 1 103 71 aact:AA02356|3end_hypothetical_protein_1614656..1614806_POSITIVE 278 87 44 53 1 aact:AA02662|3end_hypothetical_protein_1853596..1853746_POSITIVE 278 60 14 149 85 aact:AA00795|3end_iron(III)_dicitrate-binding_periplasmic_protein_precursor_545763..545913_POSITIVE 275 49 20 43 2 aact:AA00163|3end_type_IV_prepilin_peptidase;_type_II_secretion_pathway_related_protein_116772..116922_POSITIVE 270 60 15 147 85 aact:AA00475|3end_conserved_hypothetical_protein_(possible_N6-adenine-specific_methylase)_332282..332432_POSITIVE