Origin IGS: gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaattctattctaaccctttttgagaaaaaaaacaactcatagattaaagtgcaaagttcaagcttacttttgcctattgacaaaaacggattaaagctacatcatataaggc Mask Tandem Repeat Region ================================================ gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt Find is-nt database================================================ Query_seq: TDE2572:TDE2573|TDE2572:TDE2573:CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:glucose-6-phosphate isomerase:<-->:2598829..2598941 113 gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2572:TDE2573|TDE2572:TDE2573:CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:glucose-6-phosphate isomerase:<-->:2598829..2598941 113 gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2572:TDE2573|TDE2572:TDE2573:CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:glucose-6-phosphate isomerase:<-->:2598829..2598941 113 gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt Predict ORF larger than 30AA ================================================ gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt 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: 83 Start: 8 End: 37 .......ATTGACAAAAACGGATTAAAGCTACATCAT............................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 77 End: 106 ............................................................................GTTGTTTTTTTTCTCAAAAAGGGTTAGAAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2572:TDE2573|TDE2572:TDE2573:CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:glucose-6-phosphate isomerase:<-->:2598829..2598941 113 gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_002967_TDE2572_TDE2573|CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:glucose-6-phosphate isomerase|NEGATIVE:POSITIVE|[2598829,2598941]|113 HSP 1 e-value: 1.0E-43 bit: 176.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgnnnnnnnnctcaaaaagggttagaatagaattt gccttatatgatgtagctttaatccgtttttgtcaataggcaaaagtaagcttgaactttgcactttaatctatgagttgttttttttctcaaaaagggttagaatagaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCUUAUAUGAUGUAGCUUUAAUCCGUUUUUGUCAAUAGGCAAAAGUAAGCUUGAACUUUGCACUUUAAUCUAUGAGUUGUUUUUUUUCUCAAAAAGGGUUAGAAUAGAAUUU ((((....(((((.(((........)))..)))))..)))).(((((........)))))....((((((((.((((..(.....)..))))....))))))))......... (-16.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUCUAUUCUAACCCUUUUUGAGAAAAAAAACAACUCAUAGAUUAAAGUGCAAAGUUCAAGCUUACUUUUGCCUAUUGACAAAAACGGAUUAAAGCUACAUCAUAUAAGGC ..............((.((((((.((...........)).........((.(((((((........)).))))))).....)))))).))....................... ( -9.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 805 80 31 171 122 NC_002967:TDE2572|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598738..2598968_NEGATIVE 258 43 1 185 136 NC_002967:TDE2633|5end_hypothetical_protein_2674359..2674589_POSITIVE 249 66 24 53 9 NC_002967:TDE0351|5end_L-lactate_dehydrogenase_395998..396228_NEGATIVE 243 73 36 213 177 NC_002967:TDE0291|5end_hypothetical_protein_321060..321290_NEGATIVE 238 63 23 110 74 NC_002967:TDE2371|5end_iron-sulfur_cluster-binding_protein_2403583..2403813_POSITIVE 237 40 1 145 95 NC_002967:TDE0689|5end_5-methylthioribose_kinase_725690..725920_POSITIVE 235 59 13 87 33 NC_002967:TDE1381|5end_V-type_ATP_synthase_subunit_E_1421905..1422135_NEGATIVE 233 47 1 189 140 NC_002967:TDE0784|5end_ribosomal_protein_S5_813891..814121_POSITIVE 232 60 12 217 169 NC_002967:TDE1917|5end_cytidylyltransferase_domain_protein_1937394..1937624_NEGATIVE 230 47 1 174 119 NC_002967:TDE1853|5end_hypothetical_protein_1882082..1882312_NEGATIVE 228 47 1 178 120 NC_002967:TDE2627|5end_transcriptional_regulator,_TetR_family_2669140..2669370_NEGATIVE 227 105 61 175 127 NC_002967:TDE1806|5end_hypothetical_protein_1843462..1843692_NEGATIVE 226 71 32 218 174 NC_002967:TDE1678|5end_ribosomal_protein_S6_1730483..1730713_NEGATIVE 225 50 1 78 6 NC_002967:TDE0668|5end_FeS_assembly_protein_SufD_705759..705989_POSITIVE 224 68 29 187 147 NC_002967:TDE1124|5end_hypothetical_protein_1156173..1156403_NEGATIVE 222 52 12 47 11 NC_002967:TDE1434|5end_hypothetical_protein_1478462..1478692_NEGATIVE 220 63 24 73 27 NC_002967:TDE0764|5end_hypothetical_protein_804527..804757_NEGATIVE 219 41 2 46 1 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 217 63 23 140 97 NC_002967:TDE1106|5end_translation_initiation_factor_IF-2_1140882..1141112_NEGATIVE 217 80 31 84 35 NC_002967:TDE0196|5end_hypothetical_protein_232571..232801_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 73 36 98 62 NC_002967:TDE0292|3end_hypothetical_protein_321175..321325_NEGATIVE 238 63 23 54 18 NC_002967:TDE2370|3end_hypothetical_protein_2403607..2403757_POSITIVE 237 40 1 132 82 NC_002967:TDE0688|3end_hypothetical_protein_725757..725907_POSITIVE 232 63 27 136 95 NC_002967:TDE0754|3end_hypothetical_protein_794507..794657_POSITIVE 227 86 50 133 97 NC_002967:TDE2488|3end_modification_methylase,_HemK_family_2510395..2510545_NEGATIVE 226 71 32 74 30 NC_002967:TDE1679|3end_ATP_synthase_subunit_K_1730627..1730777_NEGATIVE 225 50 1 75 3 NC_002967:TDE0667|3end_FeS_assembly_protein_SufB_705836..705986_POSITIVE 220 27 1 150 121 NC_002967:TDE2632|3end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2674424..2674574_POSITIVE 217 63 23 132 89 NC_002967:TDE1107|3end_transcription_elongation_factor_NusA_1140890..1141040_NEGATIVE 213 48 2 85 41 NC_002967:TDE0612|3end_hypothetical_protein_647367..647517_NEGATIVE 211 41 4 105 68 NC_002967:TDE2320|3end_RNA_polymerase_sigma-24_factor,_putative_2356310..2356460_NEGATIVE 210 49 15 127 94 NC_002967:TDE2233|3end_iron_compound_ABC_transporter,_permease_protein,_putative_2271291..2271441_NEGATIVE 207 56 13 83 41 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 206 47 1 134 99 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 203 83 44 96 62 NC_002967:TDE0588|3end_histidine_ammonia-lyase_628053..628203_POSITIVE 202 60 16 150 116 NC_002967:TDE2536|3end_hypothetical_protein_2563341..2563491_POSITIVE 202 69 24 75 25 NC_002967:TDE2224|3end_hypothetical_protein_2264951..2265101_POSITIVE 200 49 1 146 105 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 200 67 24 49 10 NC_002967:TDE2551|3end_hypothetical_protein_2576212..2576362_NEGATIVE 198 34 2 144 98 NC_002967:TDE2165|3end_hydrogenase_accessory_protein_HypB_2197053..2197203_NEGATIVE