Origin IGS: ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtaagtgtgaaatgtctcttacaatttataaagtgtgaaataccttgctccttatgcttgataaaataagataaattgagtattattatattagttattgataaggaggtgtgataaacagttcggcacaa Mask Tandem Repeat Region ================================================ ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac Find is-nt database================================================ Query_seq: TDE1694:TDE1695|TDE1694:TDE1695:hypothetical protein:CoA-substrate-specific enzyme activase domain protein:<-<-:1749457..1749587 131 ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1694:TDE1695|TDE1694:TDE1695:hypothetical protein:CoA-substrate-specific enzyme activase domain protein:<-<-:1749457..1749587 131 ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1694:TDE1695|TDE1694:TDE1695:hypothetical protein:CoA-substrate-specific enzyme activase domain protein:<-<-:1749457..1749587 131 ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 1 End: 129 M C R T V Y H T S L S I T N I I I L N L S Y F I K H K E Q G I S H F I N C K R H F T L .. ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac 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: 86 Start: 46 End: 75 .............................................CTTGATAAAATAAGATAAATTGAGTATTAT........................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1694:TDE1695|TDE1694:TDE1695:hypothetical protein:CoA-substrate-specific enzyme activase domain protein:<-<-:1749457..1749587 131 ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_002967_TDE1694_TDE1695|hypothetical protein:CoA-substrate-specific enzyme activase domain protein|NEGATIVE:NEGATIVE|[1749457,1749587]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac ttgtgccgaactgtttatcacacctccttatcaataactaatataataatactcaatttatcttattttatcaagcataaggagcaaggtatttcacactttataaattgtaagagacatttcacacttac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUGCCGAACUGUUUAUCACACCUCCUUAUCAAUAACUAAUAUAAUAAUACUCAAUUUAUCUUAUUUUAUCAAGCAUAAGGAGCAAGGUAUUUCACACUUUAUAAAUUGUAAGAGACAUUUCACACUUAC ..(((..(((.(((((...(((.(((((((((.......((((..((((........))))..)))).......).)))))))).(((((.......)))))......)))...))))).))).))).... (-19.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAGUGUGAAAUGUCUCUUACAAUUUAUAAAGUGUGAAAUACCUUGCUCCUUAUGCUUGAUAAAAUAAGAUAAAUUGAGUAUUAUUAUAUUAGUUAUUGAUAAGGAGGUGUGAUAAACAGUUCGGCACAA ....(((((((.(((.(.(((((.(((((.....)))))........((((((((...((((..((((.(((((........))))).)))).))))...)))))))).))))).).))).))).)))).. (-23.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 120 71 211 162 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 433 28 4 198 174 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 433 28 4 199 175 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 433 28 4 98 74 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 433 30 1 100 71 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 414 27 4 188 165 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 368 28 4 176 152 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 352 28 4 74 50 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 342 28 4 187 163 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 342 28 4 77 53 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 341 33 4 163 136 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 328 37 4 172 134 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 323 27 4 154 131 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 319 29 4 204 179 NC_002967:TDE0870|5end_phosphatase/nucleotidase_892698..892928_POSITIVE 305 28 4 155 131 NC_002967:TDE1210|5end_ATP-dependent_protease_peptidase_subunit_1243329..1243559_POSITIVE 305 28 4 98 74 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 291 28 4 137 113 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 290 32 4 197 166 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 286 28 4 186 162 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 283 39 4 110 74 NC_002967:TDE1131|5end_hypothetical_protein_1163182..1163412_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 466 31 4 84 57 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 433 28 4 87 63 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 433 28 4 78 54 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 433 30 1 85 56 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 414 27 4 36 13 NC_002967:TDE0467|3end_hypothetical_protein_519006..519156_NEGATIVE 368 28 4 44 20 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 352 28 4 59 35 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 351 29 4 89 64 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 335 30 4 93 67 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 328 37 4 99 61 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 323 27 4 27 4 NC_002967:TDE1654|3end_ATP-dependent_helicase_HrpA,_putative_1704911..1705061_POSITIVE 319 29 4 88 63 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 313 31 4 94 67 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 305 28 4 88 64 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 305 28 4 34 10 NC_002967:TDE0691|3end_ABC_transporter,_ATP-binding/permease_protein_729728..729878_POSITIVE 291 28 4 84 60 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 291 28 4 61 37 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 290 32 4 95 64 NC_002967:TDE1299|3end_hypothetical_protein_1335417..1335567_NEGATIVE 286 28 4 70 46 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 286 28 4 82 58 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE