Origin IGS: cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcgttctttgaaattgttgtgtgcggaaaattttagcggctgattataggcggtttccttatgattagcaatttagccgatgaaacaaaaaacgcatttgttaatctttagtgaagaaggtttgcgctttgtgttaaactctgccggtttgatgtcgcccacggg Mask Tandem Repeat Region ================================================ cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc Find is-nt database================================================ Query_seq: AA01044:AA01045|AA01044:AA01045:A/G-specific adenine glycosylase:S-adenosylmethionine-dependent methyltransferase:->->:728039..728203 165 cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01044:AA01045|AA01044:AA01045:A/G-specific adenine glycosylase:S-adenosylmethionine-dependent methyltransferase:->->:728039..728203 165 cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01044:AA01045|AA01044:AA01045:A/G-specific adenine glycosylase:S-adenosylmethionine-dependent methyltransferase:->->:728039..728203 165 cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc Predict ORF larger than 30AA ================================================ cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc 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: 84 Start: 94 End: 123 .............................................................................................ATTGCTAATCATAAGGAAACCGCCTATAAT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01044:AA01045|AA01044:AA01045:A/G-specific adenine glycosylase:S-adenosylmethionine-dependent methyltransferase:->->:728039..728203 165 cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: aact_AA01044_AA01045|A/G-specific adenine glycosylase:S-adenosylmethionine-dependent methyltransferase|POSITIVE:POSITIVE|[728039,728203]|165 HSP 1 e-value: 7.0E-89 bit: 327.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc cccgtgggcgacatcaaaccggcagagtttaacacaaagcgcaaaccttcttcactaaagattaacaaatgcgttttttgtttcatcggctaaattgctaatcataaggaaaccgcctataatcagccgctaaaattttccgcacacaacaatttcaaagaacgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGUGGGCGACAUCAAACCGGCAGAGUUUAACACAAAGCGCAAACCUUCUUCACUAAAGAUUAACAAAUGCGUUUUUUGUUUCAUCGGCUAAAUUGCUAAUCAUAAGGAAACCGCCUAUAAUCAGCCGCUAAAAUUUUCCGCACACAACAAUUUCAAAGAACGC ...(((.(((.........((((.((....((((.((((((((.....((((.....))))........)))))))).))))...)).((......))........(((......))).......))))...........))).))).................. (-29.57) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUUCUUUGAAAUUGUUGUGUGCGGAAAAUUUUAGCGGCUGAUUAUAGGCGGUUUCCUUAUGAUUAGCAAUUUAGCCGAUGAAACAAAAAACGCAUUUGUUAAUCUUUAGUGAAGAAGGUUUGCGCUUUGUGUUAAACUCUGCCGGUUUGAUGUCGCCCACGGG ................(((((.((((............((((((((((((.(....))))))))))))).(((.(((((..((.......((((((..(((.(((((((......))))))).)))...))))))....))...))))).))).)))).))))). (-38.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 145 101 139 88 aact:AA01416|5end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_952780..953010_POSITIVE 353 41 2 54 16 aact:AA02334|5end_outer_membrane_protein_P1_1595307..1595537_POSITIVE 350 48 3 172 132 aact:AA02099|5end_50S_ribosomal_protein_L25_1429639..1429869_POSITIVE 309 50 2 66 10 aact:AA00046|5end_formate_dependent_nitrite_reductase,_cytochrome-c_type_protein_36014..36244_POSITIVE 302 47 1 201 156 aact:AA00895|5end_hypothetical_protein_621285..621515_POSITIVE 298 48 2 66 15 aact:AA00816|5end_lacZ_expression_regulator_560900..561130_POSITIVE 297 49 2 76 15 aact:AA00952|5end_hemY_protein_homolog_657541..657771_POSITIVE 294 45 1 68 19 aact:AA00695|5end_uridine_kinase_475033..475263_POSITIVE 292 43 2 57 17 aact:AA00527|5end_ATP-dependent_DNA_helicase_359371..359601_POSITIVE 291 53 11 87 48 aact:AA01610|5end_hypothetical_protein_1088811..1089041_POSITIVE 287 41 1 62 25 aact:AA00115|5end_glutamate--cysteine_ligase_(gamma-glutamylcysteine_synthetase)_(gamma-ECS)_84027..84257_POSITIVE 285 117 71 181 117 aact:AA02992|5end_RNA_methyltransferase_2090638..2090868_POSITIVE 280 50 4 68 32 aact:AA01692|5end_hexulose-6-phosphate_synthase_1149178..1149408_POSITIVE 280 29 2 84 52 aact:AA01487|5end_ATP_synthase_F1,_subunit_delta_1000114..1000344_POSITIVE 280 50 1 48 8 aact:AA00446|5end_transposase_309570..309800_POSITIVE 278 149 108 212 161 aact:AA02939|5end_phosphoserine_phosphatase_2056881..2057111_POSITIVE 278 48 1 81 35 aact:AA01327|5end_possible_LOS_biosynthesis_enzyme_(D-glycero-D-manno-heptosyl_transferase)_895568..895798_POSITIVE 278 129 86 100 56 aact:AA00989|5end_hypothetical_protein_692319..692549_POSITIVE 278 42 2 74 35 aact:AA00362|5end_30S_ribosomal_protein_S3_244847..245077_POSITIVE 277 127 85 70 23 aact:AA01939|5end_NAD(P)_transhydrogenase_subunit_beta_1311039..1311269_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 145 101 139 88 aact:AA01413|3end_conserved_hypothetical_protein_952860..953010_POSITIVE 333 48 2 85 22 aact:AA02543|3end_conserved_hypothetical_protein_1773434..1773584_POSITIVE 309 50 2 66 10 aact:AA00044|3end_formate_dependent_nitrite_reductase,_Fe-S_protein/_anaerobic_DMSO_reductase_B_36094..36244_POSITIVE 296 151 112 37 4 aact:AA01842|3end_conserved_hypothetical_protein_1238467..1238617_POSITIVE 294 45 1 55 6 aact:AA00694|3end_dCTP_deaminase_(deoxycytidine_triphosphate_deaminas)_475100..475250_POSITIVE 292 43 2 65 25 aact:AA00525|3end_hypothetical_protein_359459..359609_POSITIVE 280 29 2 68 36 aact:AA01486|3end_ATP_synthase_F1,_subunit_alpha_1000178..1000328_POSITIVE 280 50 1 45 5 aact:AA00444|3end_NTP_binding_protein_309647..309797_POSITIVE 278 48 1 72 26 aact:AA01325|3end_formamidopyrimidine-DNA_glycosylase_895639..895789_POSITIVE 278 42 2 57 18 aact:AA00361|3end_50S_ribosomal_protein_L16_244910..245060_POSITIVE 277 46 2 40 2 aact:AA02438|3end_membrane_protein;_possible_ABC_transporter_permease_protein_1683992..1684142_POSITIVE 277 127 85 56 9 aact:AA01938|3end_NAD(P)_transhydrogenase_subunit_alpha_1311105..1311255_POSITIVE 276 45 2 48 1 aact:AA01890|3end_cell-cycle_protein_1275967..1276117_POSITIVE 272 47 1 67 16 aact:AA00575|3end_shikimate_5-dehydrogenase_394093..394243_POSITIVE 271 129 81 133 86 aact:AA02253|3end_hypothetical_protein_1534786..1534936_POSITIVE 271 115 72 131 81 aact:AA01778|3end_aminopeptidase_A/I;_cytosol_aminopeptidase;_leucyl_aminopeptidase_1199965..1200115_POSITIVE 269 47 2 78 44 aact:AA01273|3end_hypothetical_protein_864588..864738_POSITIVE 269 31 1 83 56 aact:AA00933|3end_ribose_ABC_transporter,_ATP-binding_protein_645197..645347_POSITIVE 268 50 2 50 7 aact:AA01419|3end_D-ribulose-phosphate-3_epimerase_955129..955279_POSITIVE 268 48 4 143 91 aact:AA00200|3end_thymidylate_synthase_139769..139919_POSITIVE