Origin IGS: taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaagtgcggttggttttcagagcgtttttagcaacttgtattaaatcacttctggataatgggaggacgcgaaaccctcccgttatctctgtttaccagtactta Mask Tandem Repeat Region ================================================ taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta Find is-nt database================================================ Query_seq: AA01199:AA01201|AA01199:AA01201:conserved hypothetical protein:phosphatase; hydrolase:->->:822547..822652 106 taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01199:AA01201|AA01199:AA01201:conserved hypothetical protein:phosphatase; hydrolase:->->:822547..822652 106 taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01199:AA01201|AA01199:AA01201:conserved hypothetical protein:phosphatase; hydrolase:->->:822547..822652 106 taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 1 End: 102 L Y Q Y V S I V P P N R T R G N D L L S K I C T A L F A R F V L R M .... taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta 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================================================ taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 60 HP_score: -6.3 Tail_Score: -3.37259 Start: 17 End: 52 Full_Region: tattaaatcacttct ggataatgggagg acgcgaaac cctcccgttatctc tgtttaccagtactt ................ggataatgggaggacgcgaaaccctcccgttatctc...................................................... TransTerm Strand: - Conf: 75 HP_score: -10.0 Tail_Score: -3.25204 Start: 19 End: 51 Full_Region: attaaatcacttctg gataatgggagg acgcgaaac cctcccgttatc tctgtttaccagtac ..................gataatgggaggacgcgaaaccctcccgttatc....................................................... Find igs database================================================ Query_seq: AA01199:AA01201|AA01199:AA01201:conserved hypothetical protein:phosphatase; hydrolase:->->:822547..822652 106 taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: aact_AA01199_AA01201|conserved hypothetical protein:phosphatase; hydrolase|POSITIVE:POSITIVE|[822547,822652]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta taagtactggtaaacagagataacgggagggtttcgcgtcctcccattatccagaagtgatttaatacaagttgctaaaaacgctctgaaaaccaaccgcacttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUACUGGUAAACAGAGAUAACGGGAGGGUUUCGCGUCCUCCCAUUAUCCAGAAGUGAUUUAAUACAAGUUGCUAAAAACGCUCUGAAAACCAACCGCACUUUA ...((..((((...(((((.....(((((((.......)))))))..........((..((((.....))))..)).......)))))...))))...))...... (-27.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUGCGGUUGGUUUUCAGAGCGUUUUUAGCAACUUGUAUUAAAUCACUUCUGGAUAAUGGGAGGACGCGAAACCCUCCCGUUAUCUCUGUUUACCAGUACUUA ..((((((...((((...(((.((.......)).....................(((((((((((((.........))))))))))))))))...)))))))))). (-33.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 45 4 208 170 aact:AA02910|5end_ribonuclease_E_2036137..2036367_POSITIVE 324 58 16 101 60 aact:AA02632|5end_rhamnosyltransferase_1831850..1832080_POSITIVE 316 60 25 175 140 aact:AA02696|5end_formate_hydrogenlyase_maturation_protein_1879476..1879706_POSITIVE 306 53 15 144 103 aact:AA02788|5end_possible_ABC-related_substrate_binding_protein_1955402..1955632_POSITIVE 302 59 24 146 114 aact:AA02006|5end_PEP--fructosephosphotransferase_system_repressor,_DeoR_family_1363930..1364160_POSITIVE 295 42 7 182 146 aact:AA02667|5end_hypothetical_protein_1856609..1856839_POSITIVE 287 59 17 58 5 aact:AA00384|5end_conserved_hypothetical_protein_(possible_nitrogen_fixation_protein)_260108..260338_POSITIVE 285 100 53 163 111 aact:AA02597|5end_ribonuclease_D_1807124..1807354_POSITIVE 281 59 24 204 157 aact:AA02736|5end_conserved_hypothetical_protein_1917350..1917580_POSITIVE 281 100 69 116 84 aact:AA00552|5end_periplasmic_nitrate_reductase_precursor_377331..377561_POSITIVE 281 60 18 72 29 aact:AA00191|5end_conserved_hypothetical_protein_(possible_acetyltransferase,_GNAT_family)_135019..135249_POSITIVE 279 52 14 102 65 aact:AA02434|5end_membrane_protein_1678547..1678777_POSITIVE 278 100 57 163 112 aact:AA02706|5end_2-oxoglutarate_dehydrogenase_E1_component_(decarboxylase_component)_1886843..1887073_POSITIVE 278 48 3 133 77 aact:AA02385|5end_dicarboxylate-binding_periplasmic_protein_1633111..1633341_POSITIVE 277 54 13 173 140 aact:AA00729|5end_possible_hemolysin_(TlyC-like)_500204..500434_POSITIVE 272 44 8 146 109 aact:AA02747|5end_ribose-phosphate_pyrophosphokinase;_phosphoribosylpyrophosphate_synthase_1924324..1924554_POSITIVE 272 44 7 230 186 aact:AA00507|5end_hypothetical_protein_352996..353226_POSITIVE 270 45 5 162 123 aact:AA02231|5end_probable_dethiobiotin_synthetase_1_1517650..1517880_POSITIVE 267 56 12 194 142 aact:AA01607|5end_oligopeptide_transporter,_periplasmic-binding_protein_1085644..1085874_POSITIVE 265 59 14 86 31 aact:AA01890|5end_cell-cycle_protein_1274544..1274774_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 58 16 135 94 aact:AA02631|3end_undecaprenyl-phosphate_galactosephosphotransferase_homolog_1831964..1832114_POSITIVE 316 60 25 37 2 aact:AA02695|3end_hydrogenase-3_component_G_1879418..1879568_POSITIVE 306 53 15 57 16 aact:AA02787|3end_ribose_ABC_transporter,_sugar_binding_protein_1955395..1955545_POSITIVE 305 100 70 124 95 aact:AA01259|3end_protoporphyrinogen_oxidase_854943..855093_POSITIVE 295 42 7 76 40 aact:AA02666|3end_DNA_helicase_II_1856583..1856733_POSITIVE 288 51 19 72 40 aact:AA01199|3end_conserved_hypothetical_protein_822486..822636_POSITIVE 285 100 53 69 17 aact:AA02595|3end_cytochrome_c_peroxidase_1807110..1807260_POSITIVE 281 100 69 108 76 aact:AA00551|3end_hypothetical_protein_377403..377553_POSITIVE 278 48 3 75 19 aact:AA02384|3end_2-dehydro-3-deoxygluconokinase_1633133..1633283_POSITIVE 270 45 5 49 10 aact:AA02230|3end_sugar_kinase_1517617..1517767_POSITIVE 267 46 17 86 46 aact:AA02609|3end_ABC_transporter,_ATP-binding_protein/permease_1820184..1820334_POSITIVE 267 56 12 124 72 aact:AA01605|3end_hypothetical_protein_1085654..1085804_POSITIVE 267 59 12 62 1 aact:AA00342|3end_hypothetical_protein_229939..230089_POSITIVE 266 100 60 119 78 aact:AA01937|3end_sugar_fermentation_stimulation_protein_1309334..1309484_POSITIVE 265 60 12 119 61 aact:AA00550|3end_ferredoxin-type_protein_377201..377351_POSITIVE 259 39 5 50 16 aact:AA02244|3end_conserved_hypothetical_protein_(probable_DNA-binding_protein;_death-on-curing_family_protein0_1527375..1527525_POSITIVE 259 43 24 148 124 aact:AA02005|3end_vancomycin_sensitivity;_SanA_protein_1364020..1364170_POSITIVE 256 100 55 77 37 aact:AA02671|3end_gluconokinase_1858917..1859067_POSITIVE 255 48 3 88 33 aact:AA02420|3end_ISRSO11_related_transposase_1662668..1662818_POSITIVE 254 59 15 72 23 aact:AA02208|3end_tryptophan_synthase,__alpha_subunit_1503996..1504146_POSITIVE