Origin IGS: tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actcacaagttctccgtgtggtacctataatcctacataaaaaataaaaagtcaatagatatattaggaattttattaatttattaaaatttatattgactcttttacaatatcatagtatcttgaaatatctaattataattttggagggcaaa Mask Tandem Repeat Region ================================================ tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt Find is-nt database================================================ Query_seq: TDE0386:TDE0387|TDE0386:TDE0387:ABC transporter, periplasmic substrate-binding protein:(R)-hydroxyglutaryl-CoA dehydratase activator:<-->:438412..438566 155 tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0386:TDE0387|TDE0386:TDE0387:ABC transporter, periplasmic substrate-binding protein:(R)-hydroxyglutaryl-CoA dehydratase activator:<-->:438412..438566 155 tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0386:TDE0387|TDE0386:TDE0387:ABC transporter, periplasmic substrate-binding protein:(R)-hydroxyglutaryl-CoA dehydratase activator:<-->:438412..438566 155 tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 62 End: 154 ............................................................. M N F N K L I K F L I Y L L T F Y F L C R I I G T T R R T C E . Protein_Len: 31 Strand: - Start: 1 End: 93 K G E L I I I L Y K L I S H Y Q L L T L I F K L L N I F N R M .............................................................. tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt 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: 32 End: 61 ...............................ATTGACTCTTTTACAATATCATAGTATCTT.............................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 100 End: 129 ...................................................................................................ATTGACTTTTTATTTTTTATGTAGGATTAT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0386:TDE0387|TDE0386:TDE0387:ABC transporter, periplasmic substrate-binding protein:(R)-hydroxyglutaryl-CoA dehydratase activator:<-->:438412..438566 155 tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt Intra-Species Hit: Count: 1 Min: 1 Max: 155 Len: 155 Subject: NC_002967_TDE0386_TDE0387|ABC transporter, periplasmic substrate-binding protein:(R)-hydroxyglutaryl-CoA dehydratase activator|NEGATIVE:POSITIVE|[438412,438566]|155 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 155 tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgacnnnnnnnnnnnnatgtaggattataggtaccacacggagaacttgtgagt tttgccctccaaaattataattagatatttcaagatactatgatattgtaaaagagtcaatataaattttaataaattaataaaattcctaatatatctattgactttttattttttatgtaggattataggtaccacacggagaacttgtgagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGCCCUCCAAAAUUAUAAUUAGAUAUUUCAAGAUACUAUGAUAUUGUAAAAGAGUCAAUAUAAAUUUUAAUAAAUUAAUAAAAUUCCUAAUAUAUCUAUUGACUUUUUAUUUUUUAUGUAGGAUUAUAGGUACCACACGGAGAACUUGUGAGU .....(((.((....(((...(((.((((....)))))))..))).....((((((((((((......(((...((((.....))))..)))......))))))))))))........)).))).((((((((.((....))...)))))))).. (-20.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCACAAGUUCUCCGUGUGGUACCUAUAAUCCUACAUAAAAAAUAAAAAGUCAAUAGAUAUAUUAGGAAUUUUAUUAAUUUAUUAAAAUUUAUAUUGACUCUUUUACAAUAUCAUAGUAUCUUGAAAUAUCUAAUUAUAAUUUUGGAGGGCAAA ........(((((((.(((((...........)))))..................(((((((.((((((.(((((.........)))))...((((((.........)))))).......)))))).)))))))...........)))))))... (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 707 50 1 141 92 NC_002967:TDE0386|5end_ABC_transporter,_periplasmic_substrate-binding_protein_438321..438551_NEGATIVE 250 150 101 148 103 NC_002967:TDE0290|5end_hypothetical_protein_320794..321024_NEGATIVE 226 149 110 157 111 NC_002967:TDE0111|5end_hypothetical_protein_131615..131845_POSITIVE 224 50 6 135 98 NC_002967:TDE2535|5end_pyruvate_kinase_2560892..2561122_POSITIVE 219 49 1 131 93 NC_002967:TDE0349|5end_phosphoenolpyruvate_synthase,_putative_391093..391323_POSITIVE 214 150 103 150 95 NC_002967:TDE1319|5end_hypothetical_protein_1356598..1356828_POSITIVE 205 50 5 128 84 NC_002967:TDE1288|5end_CAAX_amino_terminal_protease_family_protein_1326317..1326547_POSITIVE 204 132 101 201 170 NC_002967:TDE0172|5end_undecaprenyl_pyrophosphate_phosphatase_203136..203366_POSITIVE 203 150 105 218 177 NC_002967:TDE2035|5end_glucose-1-phosphate_adenylyltransferase_2062801..2063031_POSITIVE 197 70 36 172 135 NC_002967:TDE1231|5end_hypothetical_protein_1265203..1265433_NEGATIVE 194 149 125 171 141 NC_002967:TDE1841|5end_hypothetical_protein_1871861..1872091_NEGATIVE 194 149 125 171 141 NC_002967:TDE1801|5end_hypothetical_protein_1837964..1838194_NEGATIVE 192 149 111 131 94 NC_002967:TDE2168|5end_hypothetical_protein_2201003..2201233_NEGATIVE 192 146 119 26 1 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 190 150 116 201 173 NC_002967:TDE2124|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpA_2156326..2156556_POSITIVE 190 50 6 192 148 NC_002967:TDE1290|5end_hypothetical_protein_1327399..1327629_POSITIVE 190 50 6 107 63 NC_002967:TDE1289|5end_hypothetical_protein_1327314..1327544_POSITIVE 183 50 6 55 12 NC_002967:TDE2610|5end_hypothetical_protein_2651970..2652200_NEGATIVE 183 122 84 145 98 NC_002967:TDE0298|5end_hypothetical_protein_327963..328193_POSITIVE 181 146 101 86 42 NC_002967:TDE1232|5end_hypothetical_protein_1267032..1267262_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 150 101 148 103 NC_002967:TDE0291|3end_hypothetical_protein_320794..320944_NEGATIVE 219 49 1 91 53 NC_002967:TDE0348|3end_transcriptional_regulator,_TetR_family_391133..391283_POSITIVE 211 143 110 150 108 NC_002967:TDE0110|3end_M23/M37_peptidase_domain_protein_131692..131842_POSITIVE 204 142 103 140 98 NC_002967:TDE1318|3end_hypothetical_protein_1356681..1356831_POSITIVE 204 132 101 122 91 NC_002967:TDE0171|3end_nuclease_SbcCD,_C_subunit,_putative_203137..203287_POSITIVE 186 50 6 83 32 NC_002967:TDE0467|3end_hypothetical_protein_519006..519156_NEGATIVE 180 149 122 77 51 NC_002967:TDE2399|3end_ribonuclease_P_protein_component_2425804..2425954_NEGATIVE 177 143 105 113 71 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 177 48 10 40 1 NC_002967:TDE0439|3end_hypothetical_protein_495104..495254_NEGATIVE 176 147 131 123 105 NC_002967:TDE1361|3end_hypothetical_protein_1401106..1401256_POSITIVE 176 148 120 40 17 NC_002967:TDE0719|3end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_755695..755845_POSITIVE 174 144 122 53 34 NC_002967:TDE1926|3end_hypothetical_protein_1943663..1943813_POSITIVE 174 140 91 115 76 NC_002967:TDE1784|3end_transcriptional_activator,_AraC_family_1823581..1823731_NEGATIVE 174 39 3 121 74 NC_002967:TDE0254|3end_hypothetical_protein_289312..289462_POSITIVE 172 145 121 58 28 NC_002967:TDE2752|3end_hypothetical_protein_2809470..2809620_POSITIVE 170 147 106 144 107 NC_002967:TDE2382|3end_cobinamide_kinase/cobinamide_phosphate_guanyltransferase_2412909..2413059_POSITIVE 169 60 34 30 4 NC_002967:TDE2534|3end_endonuclease_III_2560856..2561006_POSITIVE 168 150 101 139 86 NC_002967:TDE2164|3end_hypothetical_protein_2196248..2196398_NEGATIVE 167 143 105 77 40 NC_002967:TDE2156|3end_translation_initiation_factor_IF-3_2190192..2190342_NEGATIVE 167 149 101 149 101 NC_002967:TDE1684|3end_adenine_phosphoribosyltransferase_1736755..1736905_NEGATIVE