Origin IGS: cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaacaaaaaaatacaaaaaaatactttttttaattttatttattttttttgtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtaaattttattatacaagcttctttccttaaagttttataaatttaaaatatgtatacggtagtataacataatttatggcattagtacaattgtttccattatattattttagattataaattgtaagaggtataaacaaaaaaaataaataaaattaaaaaaagtatttttttgtatttttttgttgacaaccggaaaattctgatttacaatataaatatatcagtgatatatcagtaattacaaattacttaaatggaggtactg Mask Tandem Repeat Region ================================================ cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaacaaaaaaatacaaaaaaatactttttttaattttatttattttttttgtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact Find is-nt database================================================ Query_seq: TDE2366:TDE2367|TDE2366:TDE2367:high-affinity branched-chain amino acid ABC transporter, permease protein:transcriptional regulator, putative:<-->:2400949..2401219 271 cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaacaaaaaaatacaaaaaaatactttttttaattttatttattttttttgtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2366:TDE2367|TDE2366:TDE2367:high-affinity branched-chain amino acid ABC transporter, permease protein:transcriptional regulator, putative:<-->:2400949..2401219 271 cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaacaaaaaaatacaaaaaaatactttttttaattttatttattttttttgtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2366:TDE2367|TDE2366:TDE2367:high-affinity branched-chain amino acid ABC transporter, permease protein:transcriptional regulator, putative:<-->:2400949..2401219 271 cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaacaaaaaaatacaaaaaaatactttttttaattttatttattttttttgtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaacaaaaaaatacaaaaaaatactttttttaattttatttattttttttgtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 62 End: 151 ............................................................. M R I F R L S T K K Y K K I L F L I L F I F F V Y T S Y N L ........................................................................................................................ Protein_Len: 36 Strand: + Start: 49 End: 156 ................................................ M Y I V N Q N F P V V N K K I Q K N T F F N F I Y F F C L Y L L Q F I I ................................................................................................................... Protein_Len: 31 Strand: - Start: 31 End: 123 .............................. Q Y I V S I N I N Y I L I K R N D V F F Y L F I S K K I K N M .................................................................................................................................................... cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaacaaaaaaatacaaaaaaatactttttttaattttatttattttttttgtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact 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: 88 Start: 55 End: 84 ......................................................GTTGACAACCGGAAAATTCTGATTTACAAT........................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaacaaaaaaatacaaaaaaatactttttttaattttatttattttttttgtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2366:TDE2367|TDE2366:TDE2367:high-affinity branched-chain amino acid ABC transporter, permease protein:transcriptional regulator, putative:<-->:2400949..2401219 271 cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaacaaaaaaatacaaaaaaatactttttttaattttatttattttttttgtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact Intra-Species Hit: Count: 1 Min: 1 Max: 271 Len: 271 Subject: NC_002967_TDE2366_TDE2367|high-affinity branched-chain amino acid ABC transporter, permease protein:transcriptional regulator, putative|NEGATIVE:POSITIVE|[2400949,2401219]|271 HSP 1 e-value: 2.0E-74 bit: 280.0 Len: 141 Query Start:131 Query End:271 Subject Strand: POSITIVE Subject Start: 131 Subject End: 271 ..................................................................................................................................gtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact ..................................................................................................................................gtttatacctcttacaatttataatctaaaataatataatggaaacaattgtactaatgccataaattatgttatactaccgtatacatattttaaatttataaaactttaaggaaagaagcttgtataataaaatttact HSP 2 e-value: 2.0E-40 bit: 167.0 Len: 84 Query Start:1 Query End:84 Subject Strand: POSITIVE Subject Start: 1 Subject End: 84 cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaac........................................................................................................................................................................................... cagtacctccatttaagtaatttgtaattactgatatatcactgatatatttatattgtaaatcagaattttccggttgtcaac........................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUACCUCCAUUUAAGUAAUUUGUAAUUACUGAUAUAUCACUGAUAUAUUUAUAUUGUAAAUCAGAAUUUUCCGGUUGUCAACAAAAAAAUACAAAAAAAUACUUUUUUUAAUUUUAUUUAUUUUUUUUGUUUAUACCUCUUACAAUUUAUAAUCUAAAAUAAUAUAAUGGAAACAAUUGUACUAAUGCCAUAAAUUAUGUUAUACUACCGUAUACAUAUUUUAAAUUUAUAAAACUUUAAGGAAAGAAGCUUGUAUAAUAAAAUUUACU .((((..((((((...((((.((((((...(((((.(((....(((((....)))))))).)))))........(((.((.((((((((((......(((((..........)))))......)))))))))).)))))..)))))).))))...............))))))....(((((((....((..((((.(((((.((((....))))))))).))))...........((((....))))..))..)))))))......)))) (-38.27) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAAUUUUAUUAUACAAGCUUCUUUCCUUAAAGUUUUAUAAAUUUAAAAUAUGUAUACGGUAGUAUAACAUAAUUUAUGGCAUUAGUACAAUUGUUUCCAUUAUAUUAUUUUAGAUUAUAAAUUGUAAGAGGUAUAAACAAAAAAAAUAAAUAAAAUUAAAAAAAGUAUUUUUUUGUAUUUUUUUGUUGACAACCGGAAAAUUCUGAUUUACAAUAUAAAUAUAUCAGUGAUAUAUCAGUAAUUACAAAUUACUUAAAUGGAGGUACUG .((........(((((.((((((.........)))))))))))...((((.(((((((((....)))).))))).))))..))..((((((......(((((((((((((((....(((.((.((((((((..((...(((((((((((((((.(((((..........)))))))))).)))))))))).))...((((....)))).)))))))).))))).....)))))))))..((((((.....))))))...)))))))))))) (-41.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 729 50 1 141 92 NC_002967:TDE2366|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2400858..2401088_NEGATIVE 241 89 55 39 4 NC_002967:TDE2042|5end_hypothetical_protein_2072179..2072409_NEGATIVE 231 143 102 117 80 NC_002967:TDE1327|5end_hypothetical_protein_1362949..1363179_NEGATIVE 221 111 74 67 22 NC_002967:TDE0024|5end_glycosyl_hydrolase,_family_3_31092..31322_NEGATIVE 219 50 5 149 97 NC_002967:TDE0842|5end_cytoplasmic_filament_protein_A_861715..861945_POSITIVE 218 82 41 164 114 NC_002967:TDE1767|5end_hypothetical_protein_1813567..1813797_NEGATIVE 208 39 1 131 94 NC_002967:TDE2009|5end_hypothetical_protein_2030382..2030612_POSITIVE 208 111 75 225 189 NC_002967:TDE0394|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_443981..444211_POSITIVE 208 153 122 168 134 NC_002967:TDE0019|5end_formate--tetrahydrofolate_ligase_25329..25559_NEGATIVE 199 157 123 208 179 NC_002967:TDE0714|5end_capsular_polysaccharide_biosynthesis_protein_747633..747863_POSITIVE 198 67 29 34 1 NC_002967:TDE2674|5end_hypothetical_protein_2713277..2713507_NEGATIVE 189 83 49 110 73 NC_002967:TDE0581|5end_transglutaminase-like_domain_protein_616620..616850_POSITIVE 188 89 55 53 15 NC_002967:TDE1673|5end_ATP-dependent_protease_ATP-binding_subunit_1726878..1727108_POSITIVE 187 221 182 218 181 NC_002967:TDE2336|5end_sodium/dicarboxylate_symporter_family_protein_2373196..2373426_NEGATIVE 186 46 1 192 149 NC_002967:TDE1560|5end_YD_repeat_protein_1611450..1611680_POSITIVE 186 81 41 106 69 NC_002967:TDE1356|5end_lipoprotein,_putative_1396669..1396899_NEGATIVE 185 106 71 50 13 NC_002967:TDE1384|5end_cadmium-translocating_P-type_ATPase_1422765..1422995_POSITIVE 182 84 43 126 80 NC_002967:TDE1093|5end_hypothetical_protein_1127374..1127604_POSITIVE 181 160 121 122 80 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 180 99 53 98 27 NC_002967:TDE2605|5end_phosphoglycerate_mutase_family_protein_2645818..2646048_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 89 55 38 3 NC_002967:TDE2043|3end_signal_recognition_particle-docking_protein_FtsY_2072180..2072330_NEGATIVE 231 143 102 104 67 NC_002967:TDE1328|3end_hypothetical_protein_1362962..1363112_NEGATIVE 223 58 27 102 63 NC_002967:TDE0010|3end_MutT/nudix_family_protein_15226..15376_POSITIVE 221 111 74 58 13 NC_002967:TDE0025|3end_hypothetical_protein_31101..31251_NEGATIVE 218 82 41 62 12 NC_002967:TDE1768|3end_hypothetical_protein_1813669..1813819_NEGATIVE 208 39 1 84 47 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 189 83 49 126 89 NC_002967:TDE0580|3end_hypothetical_protein_616716..616866_POSITIVE 188 89 55 60 22 NC_002967:TDE1672|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_ClpP_1726965..1727115_POSITIVE 186 46 1 73 30 NC_002967:TDE1559|3end_hypothetical_protein_1611411..1611561_POSITIVE 186 251 211 51 11 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 185 106 71 56 19 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 183 212 174 118 85 NC_002967:TDE0448|3end_deoxyribose-phosphate_aldolase_506526..506676_POSITIVE 180 172 133 107 63 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE 176 65 22 48 1 NC_002967:TDE2758|3end_hypothetical_protein_2814401..2814551_POSITIVE 175 58 21 58 15 NC_002967:TDE1664|3end_hypothetical_protein_1718982..1719132_POSITIVE 174 79 31 135 74 NC_002967:TDE1677|3end_single-strand_binding_protein_1729683..1729833_NEGATIVE 174 50 2 148 104 NC_002967:TDE0607|3end_ParA_family_ATPase_644125..644275_NEGATIVE 172 83 55 44 15 NC_002967:TDE2450|3end_ankyrin_repeat_protein_2479887..2480037_POSITIVE 169 85 62 107 79 NC_002967:TDE1409|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1452381..1452531_POSITIVE 169 146 102 103 50 NC_002967:TDE0784|3end_ribosomal_protein_S5_814492..814642_POSITIVE