Origin IGS: aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatacacctctcatctgcttaaaatatcggtttaaaaaaaaataactaaagcctttttaaaattgagataaagtcaaacttttacacttgcaataaatcaggctt Mask Tandem Repeat Region ================================================ aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt Find is-nt database================================================ Query_seq: TDE1518:TDE1519|TDE1518:TDE1519:permease, putative:hypothetical protein:->->:1565636..1565740 105 aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1518:TDE1519|TDE1518:TDE1519:permease, putative:hypothetical protein:->->:1565636..1565740 105 aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1518:TDE1519|TDE1518:TDE1519:permease, putative:hypothetical protein:->->:1565636..1565740 105 aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt Predict ORF larger than 30AA ================================================ aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt 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================================================ aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1518:TDE1519|TDE1518:TDE1519:permease, putative:hypothetical protein:->->:1565636..1565740 105 aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_002967_TDE1518_TDE1519|permease, putative:hypothetical protein|POSITIVE:POSITIVE|[1565636,1565740]|105 HSP 1 e-value: 3.0E-37 bit: 155.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttannnnnnnnnaaaccgatattttaagcagatgagaggtgtatt aagcctgatttattgcaagtgtaaaagtttgactttatctcaattttaaaaaggctttagttatttttttttaaaccgatattttaagcagatgagaggtgtatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCCUGAUUUAUUGCAAGUGUAAAAGUUUGACUUUAUCUCAAUUUUAAAAAGGCUUUAGUUAUUUUUUUUUAAACCGAUAUUUUAAGCAGAUGAGAGGUGUAUU ..((((......((((....))))..((((((...((((.....((((((((((..(.....)..))))))))))..))))..)))))).......))))..... (-12.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACACCUCUCAUCUGCUUAAAAUAUCGGUUUAAAAAAAAAUAACUAAAGCCUUUUUAAAAUUGAGAUAAAGUCAAACUUUUACACUUGCAAUAAAUCAGGCUU ........(((((.....((((((....(((((...............))))).))))))...)))))..(((((.........................))))) ( -8.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 218 97 51 69 24 NC_002967:TDE0716|5end_CAAX_amino_terminal_protease_family_protein_750828..751058_POSITIVE 215 90 42 90 33 NC_002967:TDE1301|5end_DNA_repair_protein_RecN_1339116..1339346_NEGATIVE 208 100 55 208 161 NC_002967:TDE2350|5end_lipoprotein,_putative_2386661..2386891_NEGATIVE 200 100 52 200 139 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 193 97 75 43 18 NC_002967:TDE0036|5end_hypothetical_protein_42527..42757_NEGATIVE 190 78 37 149 109 NC_002967:TDE2352|5end_flagellar_hook-associated_protein_2387235..2387465_POSITIVE 190 85 44 88 37 NC_002967:TDE1495|5end_hypothetical_protein_1540216..1540446_NEGATIVE 187 39 2 172 127 NC_002967:TDE1384|5end_cadmium-translocating_P-type_ATPase_1422765..1422995_POSITIVE 184 40 4 142 109 NC_002967:TDE1895|5end_GTP-binding_protein_Era_1914963..1915193_POSITIVE 184 57 13 179 134 NC_002967:TDE1480|5end_hypothetical_protein_1525581..1525811_NEGATIVE 183 59 15 177 133 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 182 70 22 167 117 NC_002967:TDE0217|5end_methylated-DNA--protein-cysteine_methyltransferase_252548..252778_POSITIVE 181 79 33 144 100 NC_002967:TDE2785|5end_hypothetical_protein_2839182..2839412_NEGATIVE 181 46 3 230 184 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 181 78 35 68 24 NC_002967:TDE2137|5end_hypothetical_protein_2166125..2166355_POSITIVE 181 48 3 173 131 NC_002967:TDE0560|5end_hypothetical_protein_594162..594392_POSITIVE 180 47 3 134 83 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 179 42 6 37 7 NC_002967:TDE1232|5end_hypothetical_protein_1267032..1267262_NEGATIVE 177 26 1 65 36 NC_002967:TDE1020|5end_dicarboxylate_transporter,_periplasmic_dicarboxylate-binding_protein,_putative_1052593..1052823_NEGATIVE 176 38 2 222 187 NC_002967:TDE2049|5end_bacterial_extracellular_solute-binding_proteins,_family_5_2077865..2078095_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 60 21 94 46 NC_002967:TDE2668|3end_serine_hydroxymethyltransferase_2704546..2704696_NEGATIVE 200 100 52 136 75 NC_002967:TDE0691|3end_ABC_transporter,_ATP-binding/permease_protein_729728..729878_POSITIVE 191 50 2 109 69 NC_002967:TDE1364|3end_valyl-tRNA_synthetase_1407572..1407722_POSITIVE 191 98 54 64 15 NC_002967:TDE1194|3end_hypothetical_protein_1227623..1227773_POSITIVE 190 78 37 138 98 NC_002967:TDE2351|3end_hypothetical_protein_2387304..2387454_POSITIVE 184 40 4 140 107 NC_002967:TDE1894|3end_ferredoxin_1915041..1915191_POSITIVE 183 59 15 103 59 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 181 79 33 103 59 NC_002967:TDE2786|3end_DNA_polymerase_III_subunit_alpha_2839223..2839373_NEGATIVE 181 48 3 57 15 NC_002967:TDE0559|3end_hypothetical_protein_594126..594276_POSITIVE 180 47 3 53 2 NC_002967:TDE0543|3end_hypothetical_protein_583853..584003_POSITIVE 179 89 50 128 84 NC_002967:TDE2514|3end_serine/threonine_protein_phosphatase_family_protein_2539855..2540005_NEGATIVE 177 90 43 150 88 NC_002967:TDE1928|3end_hypothetical_protein_1946583..1946733_POSITIVE 177 26 1 68 39 NC_002967:TDE1021|3end_lipoprotein,_putative_1052590..1052740_NEGATIVE 172 29 2 75 48 NC_002967:TDE2068|3end_antigen,_putative_2096595..2096745_POSITIVE 170 87 52 114 86 NC_002967:TDE1875|3end_hypothetical_protein_1895806..1895956_NEGATIVE 170 43 2 99 44 NC_002967:TDE1575|3end_lipoyl_synthase_1622855..1623005_POSITIVE 170 39 15 24 1 NC_002967:TDE0404|3end_hypothetical_protein_455359..455509_NEGATIVE 169 100 53 78 31 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 169 77 53 139 115 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 169 50 1 52 2 NC_002967:TDE0803|3end_hypothetical_protein_826875..827025_POSITIVE