Origin IGS: aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaggcttacacattaaattaaaccattaataatgaagaaaggcgggatcaatttcccgtcttttttgctataatcgcccacataaatttttatgacggacttttt Mask Tandem Repeat Region ================================================ aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta Find is-nt database================================================ Query_seq: AA01715:AA01717|AA01715:AA01717:conserved hypothetical protein:fumarate hydratase, class II:->->:1161223..1161328 106 aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01715:AA01717|AA01715:AA01717:conserved hypothetical protein:fumarate hydratase, class II:->->:1161223..1161328 106 aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01715:AA01717|AA01715:AA01717:conserved hypothetical protein:fumarate hydratase, class II:->->:1161223..1161328 106 aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta Predict ORF larger than 30AA ================================================ aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta 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================================================ aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 89 HP_score: -7.1 Tail_Score: -5.23316 Start: 46 End: 65 Full_Region: ttaataatgaagaaa ggcggga tcaatt tcccgtc ttttttgctataatc .............................................ggcgggatcaatttcccgtc......................................... Find igs database================================================ Query_seq: AA01715:AA01717|AA01715:AA01717:conserved hypothetical protein:fumarate hydratase, class II:->->:1161223..1161328 106 aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: aact_AA01715_AA01717|conserved hypothetical protein:fumarate hydratase, class II|POSITIVE:POSITIVE|[1161223,1161328]|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 aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta aaaaagtccgtcataaaaatttatgtgggcgattatagcaaaaaagacgggaaattgatcccgcctttcttcattattaatggtttaatttaatgtgtaagcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGUCCGUCAUAAAAAUUUAUGUGGGCGAUUAUAGCAAAAAAGACGGGAAAUUGAUCCCGCCUUUCUUCAUUAUUAAUGGUUUAAUUUAAUGUGUAAGCCUUA .....(((((.(((((....))))))))))............((((.(((((......))))).)))).............((((((..........))))))... (-22.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGCUUACACAUUAAAUUAAACCAUUAAUAAUGAAGAAAGGCGGGAUCAAUUUCCCGUCUUUUUUGCUAUAAUCGCCCACAUAAAUUUUUAUGACGGACUUUUU ...(((.....(((((..((((....)))))))))(((((((((((((......))))))))))))).........)))..(((((....)))))........... (-24.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 68 24 170 125 aact:AA02486|5end_topoisomerase_IV,_subunit_B_1724337..1724567_POSITIVE 284 64 24 66 24 aact:AA02777|5end_tRNA-guanine_transglycosylase_1941299..1941529_POSITIVE 272 69 24 154 105 aact:AA02049|5end_hypothetical_protein_1395526..1395756_POSITIVE 271 68 25 177 138 aact:AA02144|5end_iron_(III)_ABC_transporter,_permease_protein_1467583..1467813_POSITIVE 271 79 33 95 39 aact:AA01941|5end_hypothetical_protein_1312480..1312710_POSITIVE 268 68 25 164 119 aact:AA02249|5end_thiamine_biosynthesis_protein_1528365..1528595_POSITIVE 267 50 8 71 30 aact:AA02972|5end_conserved_hypothetical_protein_(tyrosine_phenol_lyase-related_protein)_2077381..2077611_POSITIVE 264 69 21 178 128 aact:AA02845|5end_Holliday_junction_DNA_helicase_1997970..1998200_POSITIVE 262 51 17 172 132 aact:AA02748|5end_conserved_hypothetical_protein_1925359..1925589_POSITIVE 261 80 33 66 13 aact:AA01204|5end_hypothetical_protein_825015..825245_POSITIVE 260 76 38 174 135 aact:AA02706|5end_2-oxoglutarate_dehydrogenase_E1_component_(decarboxylase_component)_1886843..1887073_POSITIVE 260 76 38 48 9 aact:AA02705|5end_hypothetical_protein_1886717..1886947_POSITIVE 255 68 25 111 56 aact:AA00674|5end_nicotinate-nucleotide-dimethylbenzimidazole_phosphoribosyltransferase_461810..462040_POSITIVE 254 64 21 128 89 aact:AA00887|5end_hypothetical_protein_616739..616969_POSITIVE 253 65 21 180 129 aact:AA01166|5end_sulphite_synthesis_pathway_protein_798599..798829_POSITIVE 253 59 17 84 36 aact:AA00982|5end_aldo-keto_reductase_686526..686756_POSITIVE 250 65 28 203 160 aact:AA02954|5end_penicillin_tolerance_protein;_hydroxymethylbutenyl_pyrophosphate_reductase_2065610..2065840_POSITIVE 247 65 26 74 39 aact:AA00459|5end_hypothetical_protein_320851..321081_POSITIVE 246 70 22 201 145 aact:AA02526|5end_conserved_hypothetical_protein_1755225..1755455_POSITIVE 246 68 23 226 171 aact:AA01873|5end_mannose-6-phosphate_isomerase_1260658..1260888_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 69 24 127 78 aact:AA02048|3end_galactitol_utilization_operon_repressor_1395579..1395729_POSITIVE 271 68 25 46 7 aact:AA02142|3end_outer_membrane_protein_OprM_precursor_1467532..1467682_POSITIVE 271 79 33 75 19 aact:AA01939|3end_NAD(P)_transhydrogenase_subunit_beta_1312540..1312690_POSITIVE 268 68 25 74 29 aact:AA02246|3end_peptidase_E_1528355..1528505_POSITIVE 265 64 23 139 89 aact:AA00578|3end_DNA_topoisomerase_395201..395351_POSITIVE 263 70 27 73 25 aact:AA03015|3end_hypothetical_protein_2105251..2105401_POSITIVE 260 76 38 46 7 aact:AA02704|3end_dihydrolipoamide_succinyltransferase_1886795..1886945_POSITIVE 260 66 22 81 27 aact:AA01675|3end_probable_multidrug_resistance_protein;_multidrug-efflux_transporter_1133589..1133739_POSITIVE 255 64 21 129 88 aact:AA02422|3end_conserved_hypothetical_protein_1668426..1668576_POSITIVE 255 64 21 129 88 aact:AA02298|3end_conserved_hypothetical_protein_1571000..1571150_POSITIVE 255 64 21 129 88 aact:AA00622|3end_conserved_hypothetical_protein_430104..430254_POSITIVE 255 64 21 129 88 aact:AA00413|3end_conserved_hypothetical_protein_280554..280704_POSITIVE 253 65 21 139 88 aact:AA01165|3end_conserved_hypothetical_protein_798638..798788_POSITIVE 248 68 24 52 9 aact:AA01040|3end_possible_lipoprotein_724946..725096_POSITIVE 247 64 25 150 116 aact:AA02143|3end_hypothetical_protein_1467641..1467791_POSITIVE 246 68 23 132 77 aact:AA01872|3end_conserved_hypothetical_protein_1260644..1260794_POSITIVE 245 86 46 131 84 aact:AA00388|3end_uridine_phosphorylase;_possible_5'-methylthioadenosine_phosphorylase;_purine_nucleoside_phosphorylase_263626..263776_POSITIVE 241 69 28 105 49 aact:AA00550|3end_ferredoxin-type_protein_377201..377351_POSITIVE 241 69 23 137 91 aact:AA00408|3end_SUN_protein_(FMU_protein)_273688..273838_POSITIVE 241 67 23 138 89 aact:AA00170|3end_hypothetical_protein_121407..121557_POSITIVE