Origin IGS: attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaaggcctcctttcgtaagcataagctaacatttagaattataacagcttacctgactattgtcaagaattgatttgagaatagaaaaaactattgacaaagacagctaaattccgcattatatgatttaggaatttttacaat Mask Tandem Repeat Region ================================================ attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa Find is-nt database================================================ Query_seq: TDE0811:TDE0812|TDE0811:TDE0812:efflux protein, putative:ABC transporter, ATP-binding/permease protein:<-->:832439..832583 145 attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0811:TDE0812|TDE0811:TDE0812:efflux protein, putative:ABC transporter, ATP-binding/permease protein:<-->:832439..832583 145 attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0811:TDE0812|TDE0811:TDE0812:efflux protein, putative:ABC transporter, ATP-binding/permease protein:<-->:832439..832583 145 attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa Predict ORF larger than 30AA ================================================ attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa 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: 91 Start: 78 End: 107 .............................................................................CTTGACAATAGTCAGGTAAGCTGTTATAAT...................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 23 End: 52 ......................ATTGACAAAGACAGCTAAATTCCGCATTAT............................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0811:TDE0812|TDE0811:TDE0812:efflux protein, putative:ABC transporter, ATP-binding/permease protein:<-->:832439..832583 145 attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_002967_TDE0811_TDE0812|efflux protein, putative:ABC transporter, ATP-binding/permease protein|NEGATIVE:POSITIVE|[832439,832583]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa attgtaaaaattcctaaatcatataatgcggaatttagctgtctttgtcaatagttttttctattctcaaatcaattcttgacaatagtcaggtaagctgttataattctaaatgttagcttatgcttacgaaaggaggccttaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGUAAAAAUUCCUAAAUCAUAUAAUGCGGAAUUUAGCUGUCUUUGUCAAUAGUUUUUUCUAUUCUCAAAUCAAUUCUUGACAAUAGUCAGGUAAGCUGUUAUAAUUCUAAAUGUUAGCUUAUGCUUACGAAAGGAGGCCUUAA ..........(((((..............(((((((((((...((((..(((((......)))))..))))......((((((....))))))..)))))....))))))...(((.(((....))).)))..)))))....... (-27.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAGGCCUCCUUUCGUAAGCAUAAGCUAACAUUUAGAAUUAUAACAGCUUACCUGACUAUUGUCAAGAAUUGAUUUGAGAAUAGAAAAAACUAUUGACAAAGACAGCUAAAUUCCGCAUUAUAUGAUUUAGGAAUUUUUACAAU .(((((..((((.((((((((....)))........(((((.....((((..(.((((....)))).)......((((..(((((......)))))..))))...)))).))))).......)))))...))))..))))).... (-21.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 839 140 91 231 182 NC_002967:TDE0811|5end_efflux_protein,_putative_832348..832578_NEGATIVE 276 67 29 48 3 NC_002967:TDE1587|5end_aspartyl-tRNA_synthetase_1634033..1634263_POSITIVE 270 139 114 62 34 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 252 105 62 210 163 NC_002967:TDE1550|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_1592747..1592977_POSITIVE 247 60 21 124 88 NC_002967:TDE2614|5end_ApbE_family_protein_2657133..2657363_NEGATIVE 246 140 92 181 132 NC_002967:TDE2154|5end_50S_ribosomal_protein_L20_2189934..2190164_NEGATIVE 245 64 29 91 62 NC_002967:TDE0183|5end_ABC_transporter,_permease_protein_218591..218821_NEGATIVE 236 48 3 188 146 NC_002967:TDE2250|5end_hypothetical_protein_2288568..2288798_POSITIVE 232 139 95 151 106 NC_002967:TDE1260|5end_cholinephosphate_cytidylyltransferase/choline_kinase_1294028..1294258_POSITIVE 229 65 28 171 125 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 228 140 95 64 15 NC_002967:TDE1293|5end_TldD/PmbA_family_protein_1332003..1332233_NEGATIVE 228 70 25 189 141 NC_002967:TDE0074|5end_amino_acid_permease_family_protein_85499..85729_NEGATIVE 222 140 92 49 11 NC_002967:TDE0045|5end_ABC_transporter,_ATP-binding_protein_55113..55343_NEGATIVE 220 102 78 36 11 NC_002967:TDE1208|5end_DNA_topoisomerase_I_1240187..1240417_POSITIVE 220 50 1 204 162 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 219 77 36 51 18 NC_002967:TDE0300|5end_leucyl_aminopeptidase_330843..331073_POSITIVE 218 50 3 150 87 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 218 68 22 100 35 NC_002967:TDE1246|5end_lipoprotein,_putative_1279039..1279269_POSITIVE 217 65 27 111 74 NC_002967:TDE1178|5end_iron_compound_ABC_transporter,_ATP-binding_protein_1207913..1208143_NEGATIVE 217 49 1 216 165 NC_002967:TDE0244|5end_ABC_transporter,_ATP-binding/permease_protein_279213..279443_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 247 60 21 111 75 NC_002967:TDE2615|3end_signal_peptidase_II_2657146..2657296_NEGATIVE 247 54 11 123 80 NC_002967:TDE1263|3end_hypothetical_protein_1298136..1298286_POSITIVE 246 140 92 150 101 NC_002967:TDE2155|3end_50S_ribosomal_protein_L35_2189965..2190115_NEGATIVE 245 137 91 113 71 NC_002967:TDE2716|3end_HAD-superfamily_hydrolase,_subfamily_IA_2773931..2774081_POSITIVE 232 69 29 51 3 NC_002967:TDE1807|3end_hypothetical_protein_1843434..1843584_NEGATIVE 229 65 28 95 49 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 225 140 91 115 67 NC_002967:TDE1676|3end_ribosomal_protein_S18_1729373..1729523_NEGATIVE 224 78 39 145 102 NC_002967:TDE0406|3end_hypothetical_protein_458929..459079_POSITIVE 224 60 17 149 103 NC_002967:TDE0075|3end_sorbitol_dehydrogenase,_putative_85527..85677_NEGATIVE 221 46 13 129 97 NC_002967:TDE2495|3end_hypothetical_protein_2518735..2518885_NEGATIVE 220 50 1 127 85 NC_002967:TDE0571|3end_hypothetical_protein_603497..603647_POSITIVE 218 50 3 77 14 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 217 65 27 95 58 NC_002967:TDE1179|3end_iron_compound_ABC_transporter,_permease_protein_1207929..1208079_NEGATIVE 217 106 62 137 95 NC_002967:TDE0574|3end_surface_protein,_putative_605862..606012_POSITIVE 212 67 28 116 74 NC_002967:TDE0791|3end_DNA-directed_RNA_polymerase_alpha_subunit_818477..818627_POSITIVE 209 68 26 150 97 NC_002967:TDE1157|3end_phage_terminase,_large_subunit,_putative_1192040..1192190_NEGATIVE 208 140 92 108 55 NC_002967:TDE0967|3end_hypothetical_protein_992529..992679_POSITIVE 204 65 30 79 28 NC_002967:TDE2535|3end_pyruvate_kinase_2562387..2562537_POSITIVE 204 55 18 144 109 NC_002967:TDE0671|3end_PIN_domain_protein_711078..711228_POSITIVE 203 76 37 95 45 NC_002967:TDE2778|3end_PspC_domain_protein_2829371..2829521_NEGATIVE