Origin IGS: aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacttttttcatagtattgtcttaagtgtgtgctttgctgcacacacttaaaaactttttttggaagcttaggcttccttcaaaacttttttaggagtaagttt Mask Tandem Repeat Region ================================================ aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt Find is-nt database================================================ Query_seq: TDE2234:TDE2235|TDE2234:TDE2235:iron compound ABC transporter, periplasmic iron compound-binding protein, putative:methylaspartate ammonia-lyase:<-<-:2273336..2273439 104 aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2234:TDE2235|TDE2234:TDE2235:iron compound ABC transporter, periplasmic iron compound-binding protein, putative:methylaspartate ammonia-lyase:<-<-:2273336..2273439 104 aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2234:TDE2235|TDE2234:TDE2235:iron compound ABC transporter, periplasmic iron compound-binding protein, putative:methylaspartate ammonia-lyase:<-<-:2273336..2273439 104 aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt Predict ORF larger than 30AA ================================================ aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt 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================================================ aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -4.8 Tail_Score: -2.62263 Start: 50 End: 88 Full_Region: AAGCTTCCAAAAAAA GTTTTTAAGTGTGTGC AGCAAA GCACACACTTAAGACAA TACTATGAAAAAAGT .................................................GTTTTTAAGTGTGTGCAGCAAAGCACACACTTAAGACAA................ Find igs database================================================ Query_seq: TDE2234:TDE2235|TDE2234:TDE2235:iron compound ABC transporter, periplasmic iron compound-binding protein, putative:methylaspartate ammonia-lyase:<-<-:2273336..2273439 104 aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_002967_TDE2234_TDE2235|iron compound ABC transporter, periplasmic iron compound-binding protein, putative:methylaspartate ammonia-lyase|NEGATIVE:NEGATIVE|[2273336,2273439]|104 HSP 1 e-value: 3.0E-40 bit: 165.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aaacttactcctaaaaaagttttgaaggaagcctaagcttccnnnnnnngtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt aaacttactcctaaaaaagttttgaaggaagcctaagcttccaaaaaaagtttttaagtgtgtgcagcaaagcacacacttaagacaatactatgaaaaaagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUUACUCCUAAAAAAGUUUUGAAGGAAGCCUAAGCUUCCAAAAAAAGUUUUUAAGUGUGUGCAGCAAAGCACACACUUAAGACAAUACUAUGAAAAAAGUU .................(((.(((..((((((....)))))).........((((((((((((((......))))))))))))))))).)))............ (-31.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUUUUUCAUAGUAUUGUCUUAAGUGUGUGCUUUGCUGCACACACUUAAAAACUUUUUUUGGAAGCUUAGGCUUCCUUCAAAACUUUUUUAGGAGUAAGUUU .((((((.....(((.(((..((((((((((((......))))))))))))...........((((((....))))))..))).))).....))))))...... (-34.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 864 80 31 171 122 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 426 68 21 165 115 NC_002967:TDE2018|5end_lipoprotein,_putative_2040550..2040780_NEGATIVE 410 79 42 172 134 NC_002967:TDE2484|5end_hypothetical_protein_2507720..2507950_NEGATIVE 377 79 44 174 137 NC_002967:TDE0522|5end_hypothetical_protein_568499..568729_POSITIVE 373 50 8 147 102 NC_002967:TDE1000|5end_3-hydroxyacid_dehydrogenase_family_protein_1026763..1026993_POSITIVE 315 69 21 173 114 NC_002967:TDE0744|5end_thioredoxin_779844..780074_POSITIVE 277 60 11 154 103 NC_002967:TDE1915|5end_alcohol_dehydrogenase,_iron-containing_1933103..1933333_NEGATIVE 267 69 25 45 5 NC_002967:TDE1172|5end_hypothetical_protein_1201006..1201236_POSITIVE 263 46 1 138 92 NC_002967:TDE2566|5end_hypothetical_protein_2594187..2594417_NEGATIVE 238 68 24 209 163 NC_002967:TDE1930|5end_hypothetical_protein_1948556..1948786_NEGATIVE 225 86 41 108 61 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 225 68 26 51 7 NC_002967:TDE0575|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_607733..607963_NEGATIVE 222 66 25 90 53 NC_002967:TDE2413|5end_hypothetical_protein_2440988..2441218_NEGATIVE 220 67 21 207 166 NC_002967:TDE2382|5end_cobinamide_kinase/cobinamide_phosphate_guanyltransferase_2412278..2412508_POSITIVE 220 65 25 49 15 NC_002967:TDE1278|5end_conserved_hypothetical_protein_TIGR01440_1312788..1313018_NEGATIVE 219 42 24 208 189 NC_002967:TDE0859|5end_hypothetical_protein_880100..880330_POSITIVE 215 47 2 206 153 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 215 68 21 61 10 NC_002967:TDE0872|5end_recA_protein_894841..895071_POSITIVE 214 70 27 64 14 NC_002967:TDE2065|5end_FeoA_family_protein_2091779..2092009_NEGATIVE 214 72 44 231 201 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 50 8 90 45 NC_002967:TDE0999|3end_formate/nitrite_transporter_1026786..1026936_POSITIVE 274 67 31 41 4 NC_002967:TDE1495|3end_hypothetical_protein_1539596..1539746_NEGATIVE 267 68 28 72 32 NC_002967:TDE0340|3end_fructose-bisphosphate_aldolase_379606..379756_POSITIVE 263 46 1 127 81 NC_002967:TDE2567|3end_hypothetical_protein_2594198..2594348_NEGATIVE 229 45 4 112 74 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 225 68 26 58 14 NC_002967:TDE0576|3end_glutamyl-tRNA(Gln)_amidotransferase,_A_subunit_607726..607876_NEGATIVE 222 66 25 57 20 NC_002967:TDE2414|3end_hypothetical_protein_2441021..2441171_NEGATIVE 220 67 21 146 105 NC_002967:TDE2381|3end_histidine_kinase-related_ATPase,_putative_2412297..2412447_POSITIVE 217 68 25 116 64 NC_002967:TDE2473|3end_30S_ribosomal_protein_S21_2496587..2496737_POSITIVE 213 97 58 135 97 NC_002967:TDE1483|3end_hypothetical_protein_1529067..1529217_POSITIVE 209 60 17 98 50 NC_002967:TDE1357|3end_aldose_1-epimerase_1397830..1397980_POSITIVE 209 71 31 73 23 NC_002967:TDE1225|3end_zinc_ABC_transporter,_ATP-binding_protein_1258751..1258901_NEGATIVE 208 43 2 48 17 NC_002967:TDE2032|3end_hypothetical_protein_2059171..2059321_NEGATIVE 208 43 2 150 119 NC_002967:TDE2031|3end_hypothetical_protein_2059069..2059219_NEGATIVE 207 45 3 125 82 NC_002967:TDE2059|3end_hypothetical_protein_2086309..2086459_NEGATIVE 204 79 31 126 82 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 204 41 4 138 90 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 201 69 21 147 95 NC_002967:TDE2538|3end_hypothetical_protein_2564272..2564422_POSITIVE 201 42 3 136 93 NC_002967:TDE1180|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein_1208919..1209069_NEGATIVE 198 44 7 43 13 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE