Origin IGS: gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggttttcattcttcagtatttgtgcaatagtgcaataatcatgacgaatattatactgaaaaaatgaagagaggcttaaattaacaacgtttctcccgaaaaagtgcggttattttctacggtgaatactaagaaaaggcatattcgctagaatatccacggaatatattttacaatttaacattcattttttagaaccgcgaaatctgttgttatgctgaataaaagaatccttacgtcatgttgtttgctcgcttttgcggttaattccgcaatggcggcgccacgc Mask Tandem Repeat Region ================================================ gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc Find is-nt database================================================ Query_seq: AA01573:AA01575|AA01573:AA01575:peptide transport periplasmic protein:conserved hypothetical protein:->->:1061515..1061803 289 gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01573:AA01575|AA01573:AA01575:peptide transport periplasmic protein:conserved hypothetical protein:->->:1061515..1061803 289 gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01573:AA01575|AA01573:AA01575:peptide transport periplasmic protein:conserved hypothetical protein:->->:1061515..1061803 289 gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 14 End: 109 ............. M A E L T A K A S K Q H D V R I L L F S I T T D F A V L K N E C .................................................................................................................................................................................... Protein_Len: 31 Strand: - Start: 72 End: 164 ....................................................................... C L L L N R P E L F H I N F Q L I Y E T S I R A F I G K R L M ............................................................................................................................. gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc 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: 92 End: 121 ...........................................................................................TTTTACAATTTAACATTCATTTTTTAGAAC........................................................................................................................................................................ 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: 84 Start: 3 End: 19 ..GTGGCGCCGCCATTGCG.............................................................................................................................................................................................................................................................................. gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01573:AA01575|AA01573:AA01575:peptide transport periplasmic protein:conserved hypothetical protein:->->:1061515..1061803 289 gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc Intra-Species Hit: Count: 1 Min: 1 Max: 289 Len: 289 Subject: aact_AA01573_AA01575|peptide transport periplasmic protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1061515,1061803]|289 HSP 1 e-value: 1.0E-162 bit: 573.0 Len: 289 Query Start:1 Query End:289 Subject Strand: POSITIVE Subject Start: 1 Subject End: 289 gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc gcgtggcgccgccattgcggaattaaccgcaaaagcgagcaaacaacatgacgtaaggattcttttattcagcataacaacagatttcgcggttctaaaaaatgaatgttaaattgtaaaatatattccgtggatattctagcgaatatgccttttcttagtattcaccgtagaaaataaccgcactttttcgggagaaacgttgttaatttaagcctctcttcattttttcagtataatattcgtcatgattattgcactattgcacaaatactgaagaatgaaaacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUGGCGCCGCCAUUGCGGAAUUAACCGCAAAAGCGAGCAAACAACAUGACGUAAGGAUUCUUUUAUUCAGCAUAACAACAGAUUUCGCGGUUCUAAAAAAUGAAUGUUAAAUUGUAAAAUAUAUUCCGUGGAUAUUCUAGCGAAUAUGCCUUUUCUUAGUAUUCACCGUAGAAAAUAACCGCACUUUUUCGGGAGAAACGUUGUUAAUUUAAGCCUCUCUUCAUUUUUUCAGUAUAAUAUUCGUCAUGAUUAUUGCACUAUUGCACAAAUACUGAAGAAUGAAAACC ..(.((((((((..((((((......))))))..))).))........(((.((((((....)))))))))...(((((((.......(((((((((......((((((.............)))))).(((((((..((((.(((........))))))))))))))..)))).....)))))....((((....)))).)))))))......))).)..(((((((((.((((((.(((.((.....)).)))((((....))))...))))))))))))))).... (-65.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUUUCAUUCUUCAGUAUUUGUGCAAUAGUGCAAUAAUCAUGACGAAUAUUAUACUGAAAAAAUGAAGAGAGGCUUAAAUUAACAACGUUUCUCCCGAAAAAGUGCGGUUAUUUUCUACGGUGAAUACUAAGAAAAGGCAUAUUCGCUAGAAUAUCCACGGAAUAUAUUUUACAAUUUAACAUUCAUUUUUUAGAACCGCGAAAUCUGUUGUUAUGCUGAAUAAAAGAAUCCUUACGUCAUGUUGUUUGCUCGCUUUUGCGGUUAAUUCCGCAAUGGCGGCGCCACGC ..((((((((.(((((((((((..(....)..)))...((.....)).....))))))))..))))))))..(((.......((((((((..(...........(((((((((((.(....).)))))((((((((.((.((((((....))))))))...((((.................)))).)))))))).))))))...(((.(((((......))))).)))........)..)))))))).((.((((.((((((......)))))).))))))))).... (-68.93) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 40 1 188 145 aact:AA00381|5end_ornithine_carbamoyltransferase_257470..257700_POSITIVE 399 50 7 56 17 aact:AA02367|5end_conserved_hypothetical_protein_1623174..1623404_POSITIVE 381 189 142 136 87 aact:AA01027|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_717676..717906_POSITIVE 365 42 1 83 20 aact:AA02806|5end_leukotoxin_A;_hemolysin_A_1973922..1974152_POSITIVE 365 204 168 98 62 aact:AA00812|5end_ATPase_(PP-loop_superfamily),_confers_aluminum_resistance_558075..558305_POSITIVE 358 38 2 68 27 aact:AA02466|5end_N-acetylneuraminate_lyase_1704963..1705193_POSITIVE 344 50 1 109 53 aact:AA00163|5end_type_IV_prepilin_peptidase;_type_II_secretion_pathway_related_protein_116006..116236_POSITIVE 340 50 1 121 61 aact:AA01190|5end_glycosyl_transferase_(possible_dolichol-phosphate_mannosyltransferase)_815278..815508_POSITIVE 339 197 152 220 175 aact:AA00347|5end_50S_ribosomal_protein_L11_232137..232367_POSITIVE 337 266 221 143 86 aact:AA02970|5end_tyrosine_phenol-lyase_2076373..2076603_POSITIVE 337 38 1 75 41 aact:AA01249|5end_conserved_hypothetical_protein_(possible_phosphoesterase)_849987..850217_POSITIVE 335 42 1 132 84 aact:AA01426|5end_threonine_deaminase_(dehydratase)_958207..958437_POSITIVE 330 40 1 168 122 aact:AA01813|5end_electron_transport_complex_protein_1220949..1221179_POSITIVE 329 49 1 88 37 aact:AA01866|5end_thiamin_ABC_transporter,_permease_protein_1253313..1253543_POSITIVE 327 50 1 92 39 aact:AA01598|5end_conserved_hypothetical_protein_1078954..1079184_POSITIVE 326 37 3 189 157 aact:AA00838|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_577522..577752_POSITIVE 326 49 6 158 106 aact:AA00143|5end_gluconate_permease_(GntP_family)_102445..102675_POSITIVE 325 43 1 195 150 aact:AA02472|5end_conserved_hypothetical_protein_1707631..1707861_POSITIVE 324 40 2 142 89 aact:AA00595|5end_hypothetical_protein_407194..407424_POSITIVE 324 205 166 128 89 aact:AA00160|5end_pilA-like_biogenesis_protein_/_prepilin_peptidase_dependent_proteinD_112836..113066_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 46 1 107 61 aact:AA02014|3end_probable_hemolysin_1370977..1371127_POSITIVE 399 50 7 54 15 aact:AA02366|3end_hypothetical_protein_1623252..1623402_POSITIVE 381 189 142 149 100 aact:AA01025|3end_hypothetical_protein_717769..717919_POSITIVE 355 43 7 144 112 aact:AA00196|3end_conserved_hypothetical_protein_138015..138165_POSITIVE 344 50 1 109 53 aact:AA00162|3end_pilin_C_biogenesis_protein/protein_transport_protein_116086..116236_POSITIVE 340 50 1 121 61 aact:AA01189|3end_conserved_hypothetical_protein_(possible_glycosyl_transferase)_815358..815508_POSITIVE 339 197 152 61 16 aact:AA00345|3end_transcription_antitermination_protein_232058..232208_POSITIVE 337 266 221 107 50 aact:AA02969|3end_beta_tyrosinase_(tyrosine_phenol-lyase)_2076417..2076567_POSITIVE 335 42 1 78 30 aact:AA01424|3end_threonine_deaminase_(dehydratase)_958233..958383_POSITIVE 324 205 166 147 108 aact:AA00158|3end_ampD_signalling_protein_(N-acetylmuramyl-L-alanine_amidase)_112935..113085_POSITIVE 315 43 2 64 4 aact:AA02844|3end_Holliday_junction_DNA_helicase_1997885..1998035_POSITIVE 313 206 168 51 11 aact:AA00592|3end_conserved_hypothetical_protein_(membrane/transport_protein)_407286..407436_POSITIVE 313 42 6 151 106 aact:AA00142|3end_glycerate_kinase_102525..102675_POSITIVE 312 37 1 61 24 aact:AA02932|3end_lytic_murein_transglycosylase_A_2053544..2053694_POSITIVE 311 49 2 142 94 aact:AA02208|3end_tryptophan_synthase,__alpha_subunit_1503996..1504146_POSITIVE 309 215 172 67 16 aact:AA01703|3end_L-ribulose-phosphate_4-epimerase_1156161..1156311_POSITIVE 308 47 1 114 73 aact:AA01573|3end_peptide_transport_periplasmic_protein_1061454..1061604_POSITIVE 306 50 1 110 53 aact:AA01908|3end_conserved_hypothetical_protein_1287384..1287534_POSITIVE 306 40 3 65 28 aact:AA00647|3end_protoporphyrinogen_oxidase_443314..443464_POSITIVE 304 32 1 145 108 aact:AA02684|3end_hydrogenase_4_membrane_subunit_1871612..1871762_POSITIVE