Origin IGS: atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgacaatcacccgaccggggcagcgatacgttagtcaatattttaacccccattgtatatatcttgattttttactacttttgccgctgatttttttttcaaaagaaaaggcaaacctcgacaatat Mask Tandem Repeat Region ================================================ atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca Find is-nt database================================================ Query_seq: TF0410:TF0411|TF0410:TF0411:8-amino-7-oxononanoate synthase:methyltransferase:->->:428930..429056 127 atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0410:TF0411|TF0410:TF0411:8-amino-7-oxononanoate synthase:methyltransferase:->->:428930..429056 127 atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0410:TF0411|TF0410:TF0411:8-amino-7-oxononanoate synthase:methyltransferase:->->:428930..429056 127 atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 1 End: 90 M L S R F A F S F E K K I S G K S S K K S R Y I Q W G L K Y ..................................... Protein_Len: 40 Strand: - Start: 3 End: 122 .. N D L N A K E K S F F I L P L L L L F D L Y I C H P N F Y Q S V Y R Q G P R T M ..... atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca 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================================================ atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0410:TF0411|TF0410:TF0411:8-amino-7-oxononanoate synthase:methyltransferase:->->:428930..429056 127 atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: tfor_TF0410_TF0411|8-amino-7-oxononanoate synthase:methyltransferase|POSITIVE:POSITIVE|[428930, 429056]|127 HSP 1 e-value: 3.0E-50 bit: 198.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 atattgtcgaggtttgccttttcttttgnnnnnnnnntcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca atattgtcgaggtttgccttttcttttgaaaaaaaaatcagcggcaaaagtagtaaaaaatcaagatatatacaatgggggttaaaatattgactaacgtatcgctgccccggtcgggtgattgtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUGUCGAGGUUUGCCUUUUCUUUUGAAAAAAAAAUCAGCGGCAAAAGUAGUAAAAAAUCAAGAUAUAUACAAUGGGGGUUAAAAUAUUGACUAACGUAUCGCUGCCCCGGUCGGGUGAUUGUCA ...((((((.(((((...(((((....)))))..)))))..)))))).................((((..(((.((.(((((..........((....))......))))).))...)))..)))). (-26.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAAUCACCCGACCGGGGCAGCGAUACGUUAGUCAAUAUUUUAACCCCCAUUGUAUAUAUCUUGAUUUUUUACUACUUUUGCCGCUGAUUUUUUUUUCAAAAGAAAAGGCAAACCUCGACAAUAU ((((.....(((....)))..((((...)))).))))..............(((((........(((....))).....((((((.....(((((((....))))))).)))))).....))))).. (-17.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 120 89 41 10 tfor:TF2320|5end_hypothetical_protein_2476654..2476884_POSITIVE 334 120 98 228 203 tfor:TF1549|5end_conserved_hypothetical_protein_1653993..1654223_POSITIVE 334 120 75 59 11 tfor:TF0094|5end_alpha-glucosidase_103561..103791_POSITIVE 316 120 76 139 92 tfor:TF3088|5end_conserved_hypothetical_protein_3322512..3322742_POSITIVE 313 120 74 72 17 tfor:TF2378|5end_peptide_chain_release_factor_1_2542682..2542912_POSITIVE 307 120 75 195 134 tfor:TF1831|5end_conserved_hypothetical_protein_1980365..1980595_POSITIVE 305 119 79 207 174 tfor:TF1406|5end_transposase_1481758..1481988_POSITIVE 303 120 75 209 168 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 299 118 76 218 172 tfor:TF0587|5end_outer_membrane_protein_618319..618549_POSITIVE 298 119 74 144 100 tfor:TF1688|5end_conserved_hypothetical_protein;_possible_periplasmic_protein_1803354..1803584_POSITIVE 293 120 77 50 8 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 292 120 89 158 117 tfor:TF0406|5end_monofunctional_biosynthetic_peptidoglycan_transglycosylase_424245..424475_POSITIVE 290 120 73 199 162 tfor:TF2368|5end_uridine_phosphorylase_2533666..2533896_POSITIVE 290 119 71 223 171 tfor:TF0467|5end_acetyltransferase-related_protein_485936..486166_POSITIVE 288 120 76 158 106 tfor:TF2475|5end_GTP_pyrophosphokinase,_(p)ppGpp_synthetase_2651925..2652155_POSITIVE 288 117 78 54 14 tfor:TF0220|5end_conserved_hypothetical_protein_246230..246460_POSITIVE 287 120 77 87 37 tfor:TF2668|5end_hypothetical_protein_2842471..2842701_POSITIVE 286 118 90 89 62 tfor:TF3158|5end_inner_membrane_protein_3393729..3393959_POSITIVE 285 120 73 93 40 tfor:TF0679|5end_hypothetical_protein_721155..721385_POSITIVE 284 80 35 169 122 tfor:TF0437|5end_conserved_hypothetical_protein_460923..461153_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 120 98 142 117 tfor:TF1548|3end_thiophene_and_furan_oxidation_protein_1653987..1654137_POSITIVE 325 120 74 139 78 tfor:TF0134|3end_transposase_element_146044..146194_POSITIVE 316 120 76 129 82 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 307 120 75 151 90 tfor:TF1830|3end_3-isopropylmalate_dehydratase,_large_subunit_1980401..1980551_POSITIVE 303 120 75 120 79 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 292 120 89 141 100 tfor:TF0405|3end_conserved_hypothetical_protein_424308..424458_POSITIVE 286 118 90 67 40 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE 285 120 75 142 91 tfor:TF0108|3end_thiamine_biosynthesis_protein,_ThiF_family_116000..116150_POSITIVE 284 112 76 55 1 tfor:TF1839|3end_conserved_hypothetical_protein_1989699..1989849_POSITIVE 282 118 73 144 96 tfor:TF2572|3end_50S_ribosomal_protein_L30_2743334..2743484_POSITIVE 279 119 76 115 70 tfor:TF2149|3end_deoxyribose-phosphate_aldolase_2323110..2323260_POSITIVE 279 120 75 121 59 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 276 118 76 83 45 tfor:TF1969|3end_transcriptional_regulator,_AsnC_family_2116634..2116784_POSITIVE 276 120 97 78 49 tfor:TF1553|3end_copper_homeostasis_protein_1659681..1659831_POSITIVE 274 118 72 151 88 tfor:TF2332|3end_signal_peptidase_I_2492613..2492763_POSITIVE 271 111 73 68 28 tfor:TF2288|3end_hypothetical_protein_2442598..2442748_POSITIVE 270 120 90 127 103 tfor:TF1317|3end_hypothetical_protein_1391835..1391985_POSITIVE 269 118 89 36 4 tfor:TF2702|3end_hypothetical_protein_2876136..2876286_POSITIVE 269 120 76 139 93 tfor:TF0175|3end_hypothetical_protein_185907..186057_POSITIVE 266 120 76 51 2 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE