Origin IGS: aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtcttaagcattatatccaattataaagttttgtcaatacaaaataatggaaatttacgtaatttataagagcattttaatcggttttagtgtataatggacatcgcaaataaatcgatggaggaaaaattt Mask Tandem Repeat Region ================================================ aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac Find is-nt database================================================ Query_seq: TDE1337:TDE1338|TDE1337:TDE1338:hypothetical protein:4-diphosphocytidyl-2C-methyl-D-erythritol kinase:<-->:1374897..1375028 132 aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1337:TDE1338|TDE1337:TDE1338:hypothetical protein:4-diphosphocytidyl-2C-methyl-D-erythritol kinase:<-->:1374897..1375028 132 aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1337:TDE1338|TDE1337:TDE1338:hypothetical protein:4-diphosphocytidyl-2C-methyl-D-erythritol kinase:<-->:1374897..1375028 132 aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac Predict ORF larger than 30AA ================================================ aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac 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================================================ aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1337:TDE1338|TDE1337:TDE1338:hypothetical protein:4-diphosphocytidyl-2C-methyl-D-erythritol kinase:<-->:1374897..1375028 132 aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_002967_TDE1337_TDE1338|hypothetical protein:4-diphosphocytidyl-2C-methyl-D-erythritol kinase|NEGATIVE:POSITIVE|[1374897,1375028]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac aaatttttcctccatcgatttatttgcgatgtccattatacactaaaaccgattaaaatgctcttataaattacgtaaatttccattattttgtattgacaaaactttataattggatataatgcttaagac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUUUCCUCCAUCGAUUUAUUUGCGAUGUCCAUUAUACACUAAAACCGAUUAAAAUGCUCUUAUAAAUUACGUAAAUUUCCAUUAUUUUGUAUUGACAAAACUUUAUAAUUGGAUAUAAUGCUUAAGAC ............(((((.........)))))..(((((((........(((((((...(((.............)))...........((((((....)))))).....))))))).)))))))........ (-12.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUUAAGCAUUAUAUCCAAUUAUAAAGUUUUGUCAAUACAAAAUAAUGGAAAUUUACGUAAUUUAUAAGAGCAUUUUAAUCGGUUUUAGUGUAUAAUGGACAUCGCAAAUAAAUCGAUGGAGGAAAAAUUU .((((..((((((...((.((((.((.(((((.............(((....))).............))))).)).)))).))...))))))........(((((.........))))).))))....... (-17.17) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 781 60 11 151 102 NC_002967:TDE1337|5end_hypothetical_protein_1374806..1375036_NEGATIVE 253 59 11 145 99 NC_002967:TDE2512|5end_aldehyde_dehydrogenase_(NADP)_family_protein_2537653..2537883_POSITIVE 228 44 7 77 38 NC_002967:TDE1530|5end_hypothetical_protein_1575872..1576102_NEGATIVE 223 66 22 178 136 NC_002967:TDE2405|5end_hypothetical_protein_2432050..2432280_NEGATIVE 209 87 47 92 56 NC_002967:TDE0129|5end_PyrBI_protein_150299..150529_NEGATIVE 208 45 3 161 122 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 205 64 23 66 23 NC_002967:TDE1932|5end_hypothetical_protein_1949409..1949639_NEGATIVE 201 55 12 121 66 NC_002967:TDE0378|5end_hypothetical_protein_432164..432394_POSITIVE 200 40 3 146 90 NC_002967:TDE1704|5end_hypothetical_protein_1760588..1760818_POSITIVE 200 45 1 144 94 NC_002967:TDE1069|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1097699..1097929_NEGATIVE 194 60 11 201 152 NC_002967:TDE1266|5end_phosphoribosylaminoimidazole_synthetase_1301588..1301818_NEGATIVE 193 42 14 166 141 NC_002967:TDE1148|5end_hypothetical_protein_1186357..1186587_NEGATIVE 191 44 9 131 97 NC_002967:TDE1610|5end_DNA-binding_protein_1659496..1659726_NEGATIVE 191 98 58 126 84 NC_002967:TDE1243|5end_hemolysin_C_1275035..1275265_POSITIVE 190 38 2 174 138 NC_002967:TDE0785|5end_ribosomal_protein_L30_814417..814647_POSITIVE 189 32 6 167 144 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 187 50 3 138 92 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 186 120 71 49 12 NC_002967:TDE1906|5end_hypothetical_protein_1923883..1924113_POSITIVE 186 44 11 112 71 NC_002967:TDE1721|5end_radical_SAM_domain_protein_1775140..1775370_POSITIVE 183 34 4 128 95 NC_002967:TDE1141|5end_tail_fiber_domain_protein_1171443..1171673_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 59 11 76 30 NC_002967:TDE2511|3end_ABC_transporter,_ATP-binding/permease_protein_2537664..2537814_POSITIVE 217 55 11 130 83 NC_002967:TDE2313|3end_hypothetical_protein_2349506..2349656_NEGATIVE 208 45 3 48 9 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 203 33 3 150 123 NC_002967:TDE1882|3end_glycosyl_hydrolase,_family_1_1904907..1905057_POSITIVE 200 40 3 116 60 NC_002967:TDE1703|3end_hypothetical_protein_1760638..1760788_POSITIVE 200 45 1 143 93 NC_002967:TDE1070|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1097700..1097850_NEGATIVE 193 42 14 97 72 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 191 98 58 123 81 NC_002967:TDE1242|3end_hypothetical_protein_1275112..1275262_POSITIVE 189 32 6 122 99 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 187 50 3 141 95 NC_002967:TDE0832|3end_hypothetical_protein_853075..853225_POSITIVE 186 98 58 61 24 NC_002967:TDE2667|3end_hypothetical_protein_2704579..2704729_POSITIVE 186 44 11 124 83 NC_002967:TDE1720|3end_radical_SAM_domain_protein_1775232..1775382_POSITIVE 183 34 4 103 70 NC_002967:TDE1142|3end_phage_minor_structural_protein,_putative_1171468..1171618_NEGATIVE 182 29 8 88 69 NC_002967:TDE0289|3end_hypothetical_protein_320071..320221_NEGATIVE 180 35 2 105 63 NC_002967:TDE1447|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_1493588..1493738_POSITIVE 178 34 3 68 38 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 177 65 23 102 57 NC_002967:TDE1248|3end_hypothetical_protein_1283620..1283770_POSITIVE 177 130 81 127 66 NC_002967:TDE0308|3end_hypothetical_protein_340716..340866_POSITIVE 175 36 4 128 97 NC_002967:TDE2042|3end_hypothetical_protein_2071496..2071646_NEGATIVE 173 41 5 68 23 NC_002967:TDE0209|3end_arsenical_pump_membrane_protein,_putative_245561..245711_POSITIVE