Origin IGS: aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatccatgggaaataataccgataacaccgagccttgtttcgacaaggcgcgttttctttaaagcacggttttatgctataatcccgccactttttgtcataatttccatagagaatttcatcatcttacgataacgctt Mask Tandem Repeat Region ================================================ aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta Find is-nt database================================================ Query_seq: AA00305:AA00306|AA00305:AA00306:conserved hypothetical protein:nitrogen regulatory protein p-II:->->:207922..208062 141 aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00305:AA00306|AA00305:AA00306:conserved hypothetical protein:nitrogen regulatory protein p-II:->->:207922..208062 141 aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00305:AA00306|AA00305:AA00306:conserved hypothetical protein:nitrogen regulatory protein p-II:->->:207922..208062 141 aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 24 End: 140 ....................... M L Y G N Y D K K W R D Y S I K P C F K E N A P C R N K A R C Y R Y Y F P W I . Protein_Len: 40 Strand: - Start: 9 End: 128 ........ R L I I F N E I S I I V F L P P I I A Y F R A K F F V R R T S V L S P T I P I M ............. aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta 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: 58 End: 87 .........................................................TTTCTTTAAAGCACGGTTTTATGCTATAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -11.0 Tail_Score: -2.56426 Start: 89 End: 112 Full_Region: GTGCTTTAAAGAAAA CGCGCCTTGT CGAA ACAAGGCTCG GTGTTATCGGTATTA ........................................................................................CGCGCCTTGTCGAAACAAGGCTCG............................. Find igs database================================================ Query_seq: AA00305:AA00306|AA00305:AA00306:conserved hypothetical protein:nitrogen regulatory protein p-II:->->:207922..208062 141 aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: aact_AA00305_AA00306|conserved hypothetical protein:nitrogen regulatory protein p-II|POSITIVE:POSITIVE|[207922,208062]|141 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta aagcgttatcgtaagatgatgaaattctctatggaaattatgacaaaaagtggcgggattatagcataaaaccgtgctttaaagaaaacgcgccttgtcgaaacaaggctcggtgttatcggtattatttcccatggatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCGUUAUCGUAAGAUGAUGAAAUUCUCUAUGGAAAUUAUGACAAAAAGUGGCGGGAUUAUAGCAUAAAACCGUGCUUUAAAGAAAACGCGCCUUGUCGAAACAAGGCUCGGUGUUAUCGGUAUUAUUUCCCAUGGAUUA ...(((((((....)))))))......(((((((((((....((..((((((.(((..((((...))))..)))))))))...((.((((((((((((....)))))))...))))).)).))...)))).)))))))... (-42.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCCAUGGGAAAUAAUACCGAUAACACCGAGCCUUGUUUCGACAAGGCGCGUUUUCUUUAAAGCACGGUUUUAUGCUAUAAUCCCGCCACUUUUUGUCAUAAUUUCCAUAGAGAAUUUCAUCAUCUUACGAUAACGCUU ...((.(((((((.........((((.((((.(((((((....)))))))..(((((....))))).)))).))))((.........))...............))))))).))........................... (-25.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 100 52 177 123 aact:AA00929|5end_DNA_gyrase_subunit_B_637797..638027_POSITIVE 335 139 92 203 161 aact:AA01646|5end_hypothetical_protein_1115069..1115299_POSITIVE 333 122 88 189 162 aact:AA01774|5end_5,10-methylenetetrahydrofolate_reductase_1195015..1195245_POSITIVE 333 122 88 51 24 aact:AA01773|5end_hypothetical_protein_1194877..1195107_POSITIVE 326 97 52 64 24 aact:AA00189|5end_dihydroxynaphthoic_acid_synthase_(naphthoate_synthas)_133119..133349_POSITIVE 325 122 86 129 92 aact:AA00915|5end_xanthine-guanine_phosphoribosyltransferase_629610..629840_POSITIVE 323 100 51 98 46 aact:AA00990|5end_conserved_hypothetical_protein_692559..692789_POSITIVE 318 100 53 174 128 aact:AA00790|5end_recombination_DNA_repair_protein_542455..542685_POSITIVE 316 126 91 43 6 aact:AA00723|5end_peptidase_B_(leucyl_aminopeptidase)_496457..496687_POSITIVE 312 126 86 51 2 aact:AA01801|5end_malate_dehydrogenase_1213358..1213588_POSITIVE 305 123 89 91 64 aact:AA00738|5end_hypothetical_protein_505087..505317_POSITIVE 304 120 71 79 25 aact:AA02915|5end_thioredoxin_m_2040652..2040882_POSITIVE 304 117 72 204 162 aact:AA00918|5end_hypothetical_protein_630044..630274_POSITIVE 303 122 86 181 146 aact:AA01345|5end_conserved_hypothetical_protein_(possible_membrane_protein)_912624..912854_POSITIVE 303 115 89 46 26 aact:AA01066|5end_conserved_hypothetical_protein_738380..738610_POSITIVE 303 120 72 126 78 aact:AA00909.1|5end_hypothetical_protein_625970..626200_POSITIVE 301 139 92 231 184 aact:AA02998|5end_conserved_hypothetical_protein_2093707..2093937_POSITIVE 300 99 51 89 39 aact:AA00316|5end_conserved_hypothetical_protein_214445..214675_POSITIVE 299 123 90 65 32 aact:AA01216|5end_conserved_hypothetical_protein_831820..832050_POSITIVE 296 134 93 164 118 aact:AA01865|5end_thiamin_ABC_transporter,_periplasmic-binding_protein_1252228..1252458_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 100 52 77 23 aact:AA00927|3end_ATP-dependent_DNA_helicase_637777..637927_POSITIVE 333 122 88 36 9 aact:AA01772|3end_shikimate_5-dehydrogenase_protein_1194942..1195092_POSITIVE 323 100 51 103 51 aact:AA00989|3end_hypothetical_protein_692644..692794_POSITIVE 321 122 81 145 106 aact:AA02734|3end_leucine-responsive_regulatory_protein_1915692..1915842_POSITIVE 312 126 86 71 22 aact:AA01800|3end_hypothetical_protein_1213458..1213608_POSITIVE 305 123 89 67 40 aact:AA00737|3end_citrate_lyase,_alpha_chain_(citrase)_505143..505293_POSITIVE 296 134 93 111 65 aact:AA01863|3end_hypothetical_protein_1252255..1252405_POSITIVE 293 120 73 62 26 aact:AA01172|3end_conserved_hypothetical_protein_803847..803997_POSITIVE 291 124 85 145 102 aact:AA00468|3end_tryptophan-specific_transport_protein_/_tyrosine-specific_transport_protein_326124..326274_POSITIVE 286 108 70 47 4 aact:AA00085|3end_menaquinone-specific_isochorismate;_isochorismate_mutase_63523..63673_POSITIVE 285 100 51 127 63 aact:AA01657|3end_maltose_high-affinity_receptor_1124095..1124245_POSITIVE 284 126 90 44 6 aact:AA01825|3end_iron(III)_ABC_transporter,_permease_protein_1229493..1229643_POSITIVE 282 127 86 64 19 aact:AA01654|3end_periplasmic_maltose-binding_protein_precursor_1121163..1121313_POSITIVE 282 137 91 151 106 aact:AA01001|3end_conserved_hypothetical_protein_699974..700124_POSITIVE 280 126 89 147 117 aact:AA03010|3end_thiophene_and_furan_oxidation_protein_2102534..2102684_POSITIVE 278 121 84 141 109 aact:AA02623|3end_dTDP-D-glucose_4,6-dehydratase_1827979..1828129_POSITIVE 273 84 43 112 71 aact:AA02032|3end_hypothetical_protein_1385294..1385444_POSITIVE 272 99 54 109 47 aact:AA02946|3end_virulence_factor_protein_2060870..2061020_POSITIVE 271 120 71 74 16 aact:AA02158|3end_TonB-dependent_outer_membrane_receptor_1477317..1477467_POSITIVE 271 116 90 146 118 aact:AA01423|3end_cell_division_protein_X,_ABC_system_permease_957680..957830_POSITIVE