Origin IGS: cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaatttgtactaaagtacaataaaaattgtactaaagatagtaaaccgttttgccggttctctttttctttgccgaaaatttatcatagatcacaataaattatagttgaagaaaaaaataaaatcggatcggagagg Mask Tandem Repeat Region ================================================ cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta Find is-nt database================================================ Query_seq: TF0069:TF0070|TF0069:TF0070:conserved hypothetical protein:possible regulatory element:->->:76942..77081 140 cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0069:TF0070|TF0069:TF0070:conserved hypothetical protein:possible regulatory element:->->:76942..77081 140 cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0069:TF0070|TF0069:TF0070:conserved hypothetical protein:possible regulatory element:->->:76942..77081 140 cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta Predict ORF larger than 30AA ================================================ cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta 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================================================ cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 44 HP_score: -2.2 Tail_Score: -3.29972 Start: 77 End: 98 Full_Region: TTCGGCAAAGAAAAA GAGAACCG GCAAAA CGGTTTAC TATCTTTAGTACAAT ............................................................................GAGAACCGGCAAAACGGTTTAC.......................................... TransTerm Strand: + Conf: 71 HP_score: -7.1 Tail_Score: -3.75863 Start: 107 End: 124 Full_Region: GGTTTACTATCTTTA GTACAAT TTTT ATTGTAC TTTAGTACAAATTTT ..........................................................................................................GTACAATTTTTATTGTAC................ Find igs database================================================ Query_seq: TF0069:TF0070|TF0069:TF0070:conserved hypothetical protein:possible regulatory element:->->:76942..77081 140 cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: tfor_TF0069_TF0070|conserved hypothetical protein:possible regulatory element|POSITIVE:POSITIVE|[76942,77081]|140 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 cctctccgatccgattttannnnnnncttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta cctctccgatccgattttatttttttcttcaactataatttattgtgatctatgataaattttcggcaaagaaaaagagaaccggcaaaacggtttactatctttagtacaatttttattgtactttagtacaaatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCUCCGAUCCGAUUUUAUUUUUUUCUUCAACUAUAAUUUAUUGUGAUCUAUGAUAAAUUUUCGGCAAAGAAAAAGAGAACCGGCAAAACGGUUUACUAUCUUUAGUACAAUUUUUAUUGUACUUUAGUACAAAUUUUA ...................((((((((((.......(((((((..((...))..))))))).......))))))))))((((((......)))))).....((..((((((((....))))))))..))........... (-26.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUUUGUACUAAAGUACAAUAAAAAUUGUACUAAAGAUAGUAAACCGUUUUGCCGGUUCUCUUUUUCUUUGCCGAAAAUUUAUCAUAGAUCACAAUAAAUUAUAGUUGAAGAAAAAAAUAAAAUCGGAUCGGAGAGG .........(((((.((((((((....)))))))).....)))))..(((.....((((((...(((((((((..(...(((((((...........)))))))...)..))))))))).....))))))..)))..... (-27.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 87 42 155 98 tfor:TF0561|5end_DNA_binding_protein;_possible__HU_protein_593548..593778_POSITIVE 295 103 61 41 4 tfor:TF0301|5end_outer_membrane_protein,_TonB_dependent_receptor_325457..325687_POSITIVE 294 85 43 177 121 tfor:TF1796|5end_ABC_transporter,_ATP-binding_protein_1936492..1936722_POSITIVE 292 105 65 121 79 tfor:TF1620|5end_TPR_domain_protein_1734454..1734684_POSITIVE 272 103 62 60 14 tfor:TF3070|5end_conserved_hypothetical_protein_3294380..3294610_POSITIVE 270 88 48 75 35 tfor:TF2545|5end_hypothetical_protein_2729053..2729283_POSITIVE 267 104 64 214 167 tfor:TF1787|5end_conserved_hypothetical_protein_1926377..1926607_POSITIVE 258 96 59 160 116 tfor:TF1745|5end_hypothetical_protein_1879154..1879384_POSITIVE 258 100 52 224 188 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 255 93 52 133 91 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 255 106 62 90 41 tfor:TF0299|5end_hypothetical_protein_324821..325051_POSITIVE 254 102 63 69 30 tfor:TF1470|5end_phosphohydrolase,_Icc_family_1563144..1563374_POSITIVE 251 93 65 130 108 tfor:TF2279|5end_hypothetical_protein_2438895..2439125_POSITIVE 251 88 49 84 47 tfor:TF2127|5end_hypothetical_protein_2304038..2304268_POSITIVE 244 90 64 228 190 tfor:TF1317|5end_hypothetical_protein_1391378..1391608_POSITIVE 244 105 64 116 74 tfor:TF1228|5end_conserved_hypothetical_protein_1314103..1314333_POSITIVE 242 105 64 69 19 tfor:TF1907|5end_ADP-heptose:LPS_heptosyltransferase_II_2061579..2061809_POSITIVE 242 80 31 67 20 tfor:TF1051|5end_glycoside_hydrolase_1111974..1112204_POSITIVE 241 94 53 204 149 tfor:TF2133|5end_aspartate-semialdehyde_dehydrogenase_2310275..2310505_POSITIVE 239 107 61 175 131 tfor:TF2115|5end_conserved_hypothetical_protein;_possible_carboxylesterase_2284786..2285016_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 103 61 45 8 tfor:TF0300|3end_hypothetical_protein_325541..325691_POSITIVE 294 85 43 81 25 tfor:TF1795|3end_conserved_hypothetical_protein_1936476..1936626_POSITIVE 292 105 65 115 73 tfor:TF1619|3end_riboflavin_synthase,_beta_subunit_1734528..1734678_POSITIVE 283 87 42 148 102 tfor:TF0560|3end_DNA-binding_protein_593632..593782_POSITIVE 258 96 59 144 100 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 255 93 52 133 91 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 255 106 62 57 8 tfor:TF0298|3end_dipeptidase_324868..325018_POSITIVE 251 93 65 145 123 tfor:TF2278|3end_conserved_hypothetical_protein_2438990..2439140_POSITIVE 242 105 64 56 6 tfor:TF1906|3end_conserved_hypothetical_protein_2061646..2061796_POSITIVE 239 25 2 96 73 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE 238 50 3 147 95 tfor:TF0058|3end_conserved_hypothetical_protein_60614..60764_POSITIVE 234 93 60 36 10 tfor:TF3154|3end_conserved_hypothetical_protein_3390489..3390639_POSITIVE 233 46 2 99 51 tfor:TF2757|3end_hypothetical_protein_2942335..2942485_POSITIVE 232 110 64 68 25 tfor:TF1730|3end_diaminopimelate_decarboxylase_1855907..1856057_POSITIVE 232 110 64 140 97 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE 230 99 64 107 66 tfor:TF0696|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_740741..740891_POSITIVE 228 93 63 46 13 tfor:TF3152|3end_hypothetical_protein_3386928..3387078_POSITIVE 227 85 48 81 43 tfor:TF3009|3end_RNA_polymerase_ECF-type_sigma_factor_3229709..3229859_POSITIVE 227 98 53 144 104 tfor:TF2112|3end_glycine_cleavage_H_protein_2282573..2282723_POSITIVE 227 110 65 137 93 tfor:TF1669|3end_ATP_synthase,_gamma_subunit_1784503..1784653_POSITIVE