Origin IGS: tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg .........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 catccgctcctcagtcttcactttatgttgcaatgaatattctttcttttattcattgctagtatagcaaaatatttattttatgtcaatgaatattttataatttattcatagatgtaatgtggcggcccatattcctatggcaaagattttctttcctcttcttgacttaaacacaatatcaacccgctttaagaggcttgctgaaaaataaaaatcttgatataattaatgtattctatataatagaaaaaaggatttgataaa Mask Tandem Repeat Region ================================================ tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg Find is-nt database================================================ Query_seq: TDE0347:TDE0348|TDE0347:TDE0348:methyl-accepting chemotaxis protein DmcA:transcriptional regulator, TetR family:<-->:390330..390596 267 tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0347:TDE0348|TDE0347:TDE0348:methyl-accepting chemotaxis protein DmcA:transcriptional regulator, TetR family:<-->:390330..390596 267 tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0347:TDE0348|TDE0347:TDE0348:methyl-accepting chemotaxis protein DmcA:transcriptional regulator, TetR family:<-->:390330..390596 267 tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 57 End: 161 ........................................................ K E A L R K F R T S I T N L D L L P F F I K A M P I H A A V N C R H M .......................................................................................................... tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg 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: 89 Start: 178 End: 207 .................................................................................................................................................................................ATTGACATAAAATAAATATTTTGCTATACT............................................................ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 39 End: 68 ......................................CTTGCTGAAAAATAAAAATCTTGATATAAT....................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0347:TDE0348|TDE0347:TDE0348:methyl-accepting chemotaxis protein DmcA:transcriptional regulator, TetR family:<-->:390330..390596 267 tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg Intra-Species Hit: Count: 1 Min: 1 Max: 267 Len: 267 Subject: NC_002967_TDE0347_TDE0348|methyl-accepting chemotaxis protein DmcA:transcriptional regulator, TetR family|NEGATIVE:POSITIVE|[390330,390596]|267 HSP 1 e-value: 1.0E-149 bit: 529.0 Len: 267 Query Start:1 Query End:267 Subject Strand: POSITIVE Subject Start: 1 Subject End: 267 tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg tttatcaaatccttttttctattatatagaatacattaattatatcaagatttttatttttcagcaagcctcttaaagcgggttgatattgtgtttaagtcaagaagaggaaagaaaatctttgccataggaatatgggccgccacattacatctatgaataaattataaaatattcattgacataaaataaatattttgctatactagcaatgaataaaagaaagaatattcattgcaacataaagtgaagactgaggagcggatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUCAAAUCCUUUUUUCUAUUAUAUAGAAUACAUUAAUUAUAUCAAGAUUUUUAUUUUUCAGCAAGCCUCUUAAAGCGGGUUGAUAUUGUGUUUAAGUCAAGAAGAGGAAAGAAAAUCUUUGCCAUAGGAAUAUGGGCCGCCACAUUACAUCUAUGAAUAAAUUAUAAAAUAUUCAUUGACAUAAAAUAAAUAUUUUGCUAUACUAGCAAUGAAUAAAAGAAAGAAUAUUCAUUGCAACAUAAAGUGAAGACUGAGGAGCGGAUG ..((((...(((((..((((((...))))))..((((...((((.((((((.(((((((((((((..((........))..)))))............((((((((..(.((((.....)))).)(((((((((.(((....))).)))...))))))................))).)))))..)))))))).)))))).))))...((((((((((..........)))))))))).......))))......)))))...)))) (-54.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCCGCUCCUCAGUCUUCACUUUAUGUUGCAAUGAAUAUUCUUUCUUUUAUUCAUUGCUAGUAUAGCAAAAUAUUUAUUUUAUGUCAAUGAAUAUUUUAUAAUUUAUUCAUAGAUGUAAUGUGGCGGCCCAUAUUCCUAUGGCAAAGAUUUUCUUUCCUCUUCUUGACUUAAACACAAUAUCAACCCGCUUUAAGAGGCUUGCUGAAAAAUAAAAAUCUUGAUAUAAUUAAUGUAUUCUAUAUAAUAGAAAAAAGGAUUUGAUAAA .(((...((((...(((............((((((((((..........))))))))))..((((((.((.(((((....(((((((((.((................((((((....(((((((....))))))).))))))......(((((......((((((((.......................))))))))......))))).......)))))))))))..))))).))))))))...)))....))))...)))... (-47.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 110 61 201 152 NC_002967:TDE0347|5end_methyl-accepting_chemotaxis_protein_DmcA_390239..390469_NEGATIVE 309 110 63 51 2 NC_002967:TDE2440|5end_ABC_transporter,_ATP-binding/permease_protein,_putative_2472043..2472273_NEGATIVE 303 148 101 95 53 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 290 84 62 222 195 NC_002967:TDE1623|5end_hypothetical_protein_1671980..1672210_NEGATIVE 283 144 106 50 4 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 281 144 102 101 59 NC_002967:TDE2490|5end_primosomal_protein_N'_2514685..2514915_NEGATIVE 276 142 103 168 126 NC_002967:TDE2536|5end_hypothetical_protein_2562320..2562550_POSITIVE 268 149 118 147 117 NC_002967:TDE2008|5end_ABC_transporter,_ATP-binding/permease_protein_2028578..2028808_POSITIVE 265 144 101 71 28 NC_002967:TDE1912|5end_redox-sensing_transcriptional_repressor_Rex_1929176..1929406_POSITIVE 262 79 32 134 77 NC_002967:TDE1715|5end_phosphoglycerate_kinase_1770762..1770992_NEGATIVE 256 138 92 169 120 NC_002967:TDE1392|5end_hypothetical_protein_1432002..1432232_POSITIVE 255 105 61 191 150 NC_002967:TDE2779|5end_hypothetical_protein_2830425..2830655_NEGATIVE 253 156 124 183 150 NC_002967:TDE1743|5end_chromate_transport_protein_1798503..1798733_NEGATIVE 253 88 41 152 102 NC_002967:TDE0980|5end_asparaginyl-tRNA_synthetase_1005400..1005630_NEGATIVE 250 104 61 151 88 NC_002967:TDE0969|5end_hypothetical_protein_993260..993490_POSITIVE 245 92 55 50 13 NC_002967:TDE1611|5end_hypothetical_protein_1659701..1659931_POSITIVE 245 85 49 66 29 NC_002967:TDE0136|5end_hypothetical_protein_156287..156517_POSITIVE 244 146 109 193 145 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 243 96 56 208 168 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 242 110 63 201 155 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 139 97 111 63 NC_002967:TDE0603|3end_hypothetical_protein_641885..642035_POSITIVE 294 108 68 86 41 NC_002967:TDE0114|3end_iron-dependent_transcriptional_regulator_133581..133731_NEGATIVE 290 84 62 131 104 NC_002967:TDE1624|3end_glycine_dehydrogenase_subunit_2_1672071..1672221_NEGATIVE 283 144 106 80 34 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 281 144 102 81 39 NC_002967:TDE2491|3end_DNA_polymerase_domain_protein_2514705..2514855_NEGATIVE 268 149 118 130 100 NC_002967:TDE2007|3end_ABC_transporter,_ATP-binding/permease_protein_2028641..2028791_POSITIVE 260 110 61 106 45 NC_002967:TDE0972|3end_comF-related_protein_997961..998111_POSITIVE 257 144 101 73 26 NC_002967:TDE2082|3end_hypothetical_protein_2112489..2112639_NEGATIVE 255 105 61 108 67 NC_002967:TDE2780|3end_hypothetical_protein_2830508..2830658_NEGATIVE 250 116 77 130 93 NC_002967:TDE1193|3end_hypothetical_protein_1219526..1219676_NEGATIVE 250 116 77 130 93 NC_002967:TDE0579|3end_hypothetical_protein_609898..610048_NEGATIVE 248 102 63 93 43 NC_002967:TDE1931|3end_cytidine_deaminase_1949020..1949170_POSITIVE 248 110 62 144 83 NC_002967:TDE1863|3end_Holliday_junction_DNA_helicase_RuvA_1887974..1888124_NEGATIVE 248 110 64 103 55 NC_002967:TDE1343|3end_trypsin_domain/PDZ_domain_protein_1382236..1382386_POSITIVE 246 103 63 76 27 NC_002967:TDE1727|3end_hypothetical_protein_1780774..1780924_NEGATIVE 245 84 47 52 15 NC_002967:TDE1716|3end_glyoxalase_family_protein_1770851..1771001_NEGATIVE 245 85 49 76 39 NC_002967:TDE0135|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_156377..156527_POSITIVE 243 110 63 76 30 NC_002967:TDE2317|3end_hemolysin_III_2354118..2354268_NEGATIVE 240 143 102 133 93 NC_002967:TDE1651|3end_BioY_family_protein_1698121..1698271_NEGATIVE 237 108 64 53 15 NC_002967:TDE1485|3end_hypothetical_protein_1530382..1530532_POSITIVE