Origin IGS: taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatctatatccttttcatacacttaaaacggatttttagattataaatgatcttatatattaagtgccaattatttgtatggttcgacaggattttatatgttta Mask Tandem Repeat Region ================================================ taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt Find is-nt database================================================ Query_seq: AA00015:AA00017|AA00015:AA00017:malate dehydrogenase:hypothetical protein:->->:8394..8498 105 taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00015:AA00017|AA00015:AA00017:malate dehydrogenase:hypothetical protein:->->:8394..8498 105 taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00015:AA00017|AA00015:AA00017:malate dehydrogenase:hypothetical protein:->->:8394..8498 105 taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt Predict ORF larger than 30AA ================================================ taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt 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================================================ taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00015:AA00017|AA00015:AA00017:malate dehydrogenase:hypothetical protein:->->:8394..8498 105 taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: aact_AA00015_AA00017|malate dehydrogenase:hypothetical protein|POSITIVE:POSITIVE|[8394,8498]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt taaacatataaaatcctgtcgaaccatacaaataattggcacttaatatataagatcatttataatctaaaaatccgttttaagtgtatgaaaaggatatagatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAUAUAAAAUCCUGUCGAACCAUACAAAUAAUUGGCACUUAAUAUAUAAGAUCAUUUAUAAUCUAAAAAUCCGUUUUAAGUGUAUGAAAAGGAUAUAGAUU ............(((((.......((((((..(((.(((.........((((((....))))))..........)))..)))..))))))...)))))....... (-11.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUAUAUCCUUUUCAUACACUUAAAACGGAUUUUUAGAUUAUAAAUGAUCUUAUAUAUUAAGUGCCAAUUAUUUGUAUGGUUCGACAGGAUUUUAUAUGUUUA .......(((((..(((((((..(((...((...(((((..(((((......)))))..)))))..))..)))..)))))))......)))))............ (-14.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 40 8 194 166 aact:AA02670|5end_hypothetical_protein_1858049..1858279_POSITIVE 212 43 17 64 37 aact:AA02358|5end_homoserine_kinase_1617128..1617358_POSITIVE 208 44 15 215 177 aact:AA01338|5end_hypothetical_protein_904967..905197_POSITIVE 208 59 11 227 173 aact:AA00417|5end_outer_membrane_lipoprotein_precursor_(probable_D-methionine-binding_lipoprotein)_283389..283619_POSITIVE 207 45 5 45 8 aact:AA02250|5end_possible_cytochrome_c-type_protein_1530125..1530355_POSITIVE 205 42 13 151 119 aact:AA01396|5end_saccharide_biosynthesis_regulatory_protein_943760..943990_POSITIVE 196 44 4 192 151 aact:AA00268|5end_acyl_carrier_protein_(ACP)_188104..188334_POSITIVE 194 44 14 41 4 aact:AA00267|5end_hypothetical_protein_187953..188183_POSITIVE 191 96 64 102 66 aact:AA00200|5end_thymidylate_synthase_138892..139122_POSITIVE 188 48 16 54 18 aact:AA02205|5end_short_chain_dehydrogenase/reductase_1501170..1501400_POSITIVE 186 41 5 217 174 aact:AA00605|5end_CDP-diglyceride_pyrophosphorylase_410930..411160_POSITIVE 184 41 16 81 57 aact:AA00448|5end_C-terminal_region_of_competence_protein_M_312268..312498_POSITIVE 182 90 49 172 135 aact:AA01444|5end_ISRS011/IS150_related_transposase,_orfB_969159..969389_POSITIVE 180 96 52 65 18 aact:AA00378|5end_leucine-responsive_regulatory_protein_(transcription_regulator)_254324..254554_POSITIVE 179 41 6 100 52 aact:AA00816|5end_lacZ_expression_regulator_560900..561130_POSITIVE 177 53 13 97 56 aact:AA01767|5end_conserved_hypothetical_protein_1192528..1192758_POSITIVE 176 56 13 113 74 aact:AA01418|5end_conserved_hypothetical_protein_953951..954181_POSITIVE 173 42 17 89 60 aact:AA01024|5end_thiamine_biosynthesis_lipoprotein_precursor_716437..716667_POSITIVE 173 57 16 115 75 aact:AA00964|5end_phosphoenolpyruvate_carboxykinase/carboxylase_672675..672905_POSITIVE 173 40 15 193 169 aact:AA00695|5end_uridine_kinase_475033..475263_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 43 5 77 36 aact:AA02514|3end_esterase/lipase_1748378..1748528_POSITIVE 220 96 51 53 13 aact:AA02012|3end_peptide_methionine_sulfoxide_reductase_1369469..1369619_POSITIVE 212 43 17 48 21 aact:AA02357|3end_bifunctional_protein:_aspartokinase_I;_homoserine_dehydrogenaseI_1617192..1617342_POSITIVE 205 42 13 48 16 aact:AA01395|3end_conserved_hypothetical_protein_943737..943887_POSITIVE 196 44 4 151 110 aact:AA00267|3end_hypothetical_protein_188143..188293_POSITIVE 188 48 16 66 30 aact:AA02204|3end_hypothetical_protein_1501262..1501412_POSITIVE 182 90 49 126 89 aact:AA01442|3end_phosphatidylserine_synthetase_969193..969343_POSITIVE 177 53 13 125 84 aact:AA01765|3end_Mu-like_prophage_FluMu_transposase_A_1192636..1192786_POSITIVE 176 56 13 110 71 aact:AA01417|3end_probable_4-diphosphocytidyl-2C-methyl-D-erthyritol_synthase_(MEP_cytidyltransferase)_(MCT)_954028..954178_POSITIVE 173 57 16 44 4 aact:AA00962|3end_exopolyphosphatase_(metaphosphatase)_672684..672834_POSITIVE 173 56 15 105 58 aact:AA00576|3end_conserved_hypothetical_protein_(possible_translation_factor)_394648..394798_POSITIVE 165 55 16 101 58 aact:AA00605|3end_CDP-diglyceride_pyrophosphorylase_411876..412026_POSITIVE 161 41 14 75 55 aact:AA00130|3end_mercuric_transport_protein_(periplasmic_mercury_ion_binding_protein)_(mercury_scavenger_protein)_94521..94671_POSITIVE 161 41 14 106 86 aact:AA00129|3end_hypothetical_protein_94552..94702_POSITIVE 158 41 12 124 95 aact:AA01048|3end_iron_binding_protein_afuA,_periplasmic_protein_730497..730647_POSITIVE 158 41 15 35 3 aact:AA00491|3end_haemin_storage_system_343493..343643_POSITIVE 157 58 15 127 92 aact:AA02687|3end_hydrogenase-4_component_D_1874043..1874193_POSITIVE 157 41 11 49 15 aact:AA00241|3end_formate_acetyltransferase_activating_enzyme_(anaerobic_ribonucleoside-triphosphate_reductase_activating_protein)_172090..172240_POSITIVE 156 99 62 65 23 aact:AA02585|3end_hypothetical_protein_1799093..1799243_POSITIVE 155 21 4 27 6 aact:AA02768|3end_conserved_hypothetical_protein_1935805..1935955_POSITIVE