Origin IGS: agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtgaaaaaataaaaatttggaggaaaaataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatttttcctccaaatttttattttttcacaccattgcttatattcttcataagaagtttttatagtatcagcaatacttctgggaacaagttttgcacgtttgaaagctgattctgcatattcaaaataatgacttccagctttgcctaaagccataccaatct Mask Tandem Repeat Region ================================================ agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtgaaaaaataaaaatttggaggaaaaataa Find is-nt database================================================ Query_seq: TDE1569:TDE1570|TDE1569:TDE1570:hypothetical protein:hypothetical protein:->->:1620036..1620201 166 agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtgaaaaaataaaaatttggaggaaaaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1569:TDE1570|TDE1569:TDE1570:hypothetical protein:hypothetical protein:->->:1620036..1620201 166 agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtgaaaaaataaaaatttggaggaaaaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1569:TDE1570|TDE1569:TDE1570:hypothetical protein:hypothetical protein:->->:1620036..1620201 166 agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtgaaaaaataaaaatttggaggaaaaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtgaaaaaataaaaatttggaggaaaaataa Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 3 End: 164 .. M G M A L G K A G S H Y F E Y A E S A F K R A K L V P R S I A D T I K T S Y E E Y K Q W C E K I K I W R K N .. Protein_Len: 36 Strand: - Start: 57 End: 164 ........................................................ S E F T C F K N G S T N S I S Y F S R I F F I L L P T F F Y F N P P F M .. agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtgaaaaaataaaaatttggaggaaaaataa 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================================================ agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtgaaaaaataaaaatttggaggaaaaataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1569:TDE1570|TDE1569:TDE1570:hypothetical protein:hypothetical protein:->->:1620036..1620201 166 agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtgaaaaaataaaaatttggaggaaaaataa Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_002967_TDE1569_TDE1570|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1620036,1620201]|166 HSP 1 e-value: 9.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtg............................ agattggtatggctttaggcaaagctggaagtcattattttgaatatgcagaatcagctttcaaacgtgcaaaacttgttcccagaagtattgctgatactataaaaacttcttatgaagaatataagcaatggtgtg............................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUGGUAUGGCUUUAGGCAAAGCUGGAAGUCAUUAUUUUGAAUAUGCAGAAUCAGCUUUCAAACGUGCAAAACUUGUUCCCAGAAGUAUUGCUGAUACUAUAAAAACUUCUUAUGAAGAAUAUAAGCAAUGGUGUG ........((((((((.(((...))).))))))))...((((((...((.......)).))))))...((((.((((........)))).))))..(((((((.....((((....))))..........))))))). (-25.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACACCAUUGCUUAUAUUCUUCAUAAGAAGUUUUUAUAGUAUCAGCAAUACUUCUGGGAACAAGUUUUGCACGUUUGAAAGCUGAUUCUGCAUAUUCAAAAUAAUGACUUCCAGCUUUGCCUAAAGCCAUACCAAUCU ......((((((.(((((((((....)))).......))))).)))))).....(((....(((((.......((((((.((.......))...)))))).....)))))...(((((....)))))....))).... (-21.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 97 54 129 81 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 251 58 11 211 171 NC_002967:TDE1884|5end_hypothetical_protein_1906857..1907087_NEGATIVE 246 50 5 139 99 NC_002967:TDE1125|5end_TPR_domain_protein_1157557..1157787_NEGATIVE 240 96 57 70 30 NC_002967:TDE0408|5end_oxidoreductase,_NAD-binding_461372..461602_NEGATIVE 239 110 63 111 66 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 236 49 4 195 142 NC_002967:TDE0353|5end_lipase/acylhydrolase,_GDSL_family_398338..398568_NEGATIVE 235 50 8 50 8 NC_002967:TDE2146|5end_hydrolase,_alpha/beta_fold_family_2183060..2183290_POSITIVE 233 58 11 206 147 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 231 85 47 51 11 NC_002967:TDE1751|5end_ribosomal_protein_L21_1804142..1804372_NEGATIVE 231 42 4 158 115 NC_002967:TDE0959|5end_hypothetical_protein_981935..982165_POSITIVE 229 58 11 201 159 NC_002967:TDE2607|5end_hypothetical_protein_2648586..2648816_POSITIVE 229 90 50 54 5 NC_002967:TDE2349|5end_hypothetical_protein_2385940..2386170_NEGATIVE 228 60 13 182 138 NC_002967:TDE2245|5end_DNA_topoisomerase_IV_subunit_B_2284240..2284470_POSITIVE 226 60 11 219 169 NC_002967:TDE0845|5end_conserved_hypothetical_protein_TIGR00266_867795..868025_POSITIVE 224 98 56 67 22 NC_002967:TDE0883|5end_16S_rRNA_processing_protein_RimM_901685..901915_POSITIVE 224 98 57 73 29 NC_002967:TDE0795|5end_hypothetical_protein_819974..820204_NEGATIVE 223 58 18 228 181 NC_002967:TDE2475|5end_MATE_efflux_family_protein_2498521..2498751_NEGATIVE 222 29 1 199 169 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 220 99 54 62 18 NC_002967:TDE0014|5end_hypothetical_protein_18790..19020_POSITIVE 218 48 4 77 24 NC_002967:TDE0033|5end_DNA-binding_response_regulator_40696..40926_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 97 54 119 71 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 272 60 17 118 60 NC_002967:TDE2777|3end_hypothetical_protein_2829351..2829501_POSITIVE 249 49 5 107 58 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 241 100 54 91 34 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 240 113 76 45 4 NC_002967:TDE0568|3end_hypothetical_protein_599228..599378_POSITIVE 239 110 63 147 102 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 234 70 22 45 2 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 233 58 11 95 36 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 233 110 63 69 19 NC_002967:TDE1992|3end_OmpA_family_protein_2010902..2011052_POSITIVE 232 50 4 76 29 NC_002967:TDE0876|3end_hypothetical_protein_898339..898489_NEGATIVE 230 59 11 150 87 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 229 58 11 86 44 NC_002967:TDE2606|3end_urocanate_hydratase_2648551..2648701_POSITIVE 227 31 11 29 4 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 226 60 11 117 67 NC_002967:TDE0844|3end_pyruvate_phosphate_dikinase,_putative_867773..867923_POSITIVE 224 59 11 144 96 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 224 98 56 64 19 NC_002967:TDE0882|3end_hypothetical_protein_901762..901912_POSITIVE 222 33 9 51 23 NC_002967:TDE0621|3end_MATE_efflux_family_protein_654776..654926_POSITIVE 221 35 1 48 19 NC_002967:TDE1967|3end_hypothetical_protein_1982533..1982683_POSITIVE 218 48 4 60 7 NC_002967:TDE0034|3end_hypothetical_protein_40713..40863_NEGATIVE 217 30 7 112 84 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE