Origin IGS: aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagcttaatataacacagtttgcctggggaatcaagaacagcttttttttcggttagatttaacttgaggcaatgcgagctctttacagactgactcattttaattagaattaaaaaacgtttattgtaacattttaagaggtatcgtatttt Mask Tandem Repeat Region ================================================ aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt Find is-nt database================================================ Query_seq: TDE2323:TDE2324|TDE2323:TDE2324:mechanosensitive ion channel family protein:DNA-binding response regulator:<-->:2359175..2359327 153 aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2323:TDE2324|TDE2323:TDE2324:mechanosensitive ion channel family protein:DNA-binding response regulator:<-->:2359175..2359327 153 aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2323:TDE2324|TDE2323:TDE2324:mechanosensitive ion channel family protein:DNA-binding response regulator:<-->:2359175..2359327 153 aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 4 End: 153 ... M R Y L L K C Y N K R F L I L I K M S Q S V K S S H C L K L N L T E K K A V L D S P G K L C Y I K L aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt 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: 85 Start: 43 End: 72 ..........................................CTTTACAGACTGACTCATTTTAATTAGAAT................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 118 End: 147 .....................................................................................................................CTTGATTCCCCAGGCAAACTGTGTTATATT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2323:TDE2324|TDE2323:TDE2324:mechanosensitive ion channel family protein:DNA-binding response regulator:<-->:2359175..2359327 153 aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_002967_TDE2323_TDE2324|mechanosensitive ion channel family protein:DNA-binding response regulator|NEGATIVE:POSITIVE|[2359175,2359327]|153 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgnnnnnnnngctgttcttgattccccaggcaaactgtgttatattaagctt aaaatacgatacctcttaaaatgttacaataaacgttttttaattctaattaaaatgagtcagtctgtaaagagctcgcattgcctcaagttaaatctaaccgaaaaaaaagctgttcttgattccccaggcaaactgtgttatattaagctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUACGAUACCUCUUAAAAUGUUACAAUAAACGUUUUUUAAUUCUAAUUAAAAUGAGUCAGUCUGUAAAGAGCUCGCAUUGCCUCAAGUUAAAUCUAACCGAAAAAAAAGCUGUUCUUGAUUCCCCAGGCAAACUGUGUUAUAUUAAGCUU ..((((..((((.....((((((((......))))))))..................(((..(((((..((((((..((.((.......((((....)))).......)).)).)))))).......)))))..)))))))..))))...... (-21.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCUUAAUAUAACACAGUUUGCCUGGGGAAUCAAGAACAGCUUUUUUUUCGGUUAGAUUUAACUUGAGGCAAUGCGAGCUCUUUACAGACUGACUCAUUUUAAUUAGAAUUAAAAAACGUUUAUUGUAACAUUUUAAGAGGUAUCGUAUUUU ..((((..........((((((.(((..(((..(((.....))).)))..))).)))))).......)))).((((((.((((((((((...(((...(((((((....)))))))...)))..))))).......)))))...))))))... (-24.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 854 120 71 211 162 NC_002967:TDE2323|5end_mechanosensitive_ion_channel_family_protein_2359084..2359314_NEGATIVE 348 104 66 183 142 NC_002967:TDE0968|5end_translation_elongation_factor_P_993126..993356_NEGATIVE 340 104 66 192 154 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 308 126 81 212 168 NC_002967:TDE1114|5end_transcriptional_regulator,_TetR_family_1148905..1149135_NEGATIVE 299 85 44 61 25 NC_002967:TDE1441|5end_dTDP-glucose_4,6-dehydratase_1486247..1486477_POSITIVE 278 115 74 223 182 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 268 99 58 198 159 NC_002967:TDE1493|5end_chemotaxis_protein_CheX_1538590..1538820_POSITIVE 260 134 95 48 12 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 259 90 57 40 11 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 258 115 72 178 121 NC_002967:TDE2534|5end_endonuclease_III_2560144..2560374_POSITIVE 257 91 55 162 128 NC_002967:TDE0023|5end_acetyltransferase,_GNAT_family_29419..29649_NEGATIVE 253 135 99 31 2 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 251 89 43 203 157 NC_002967:TDE0462|5end_metallo-beta-lactamase_family_protein_516987..517217_NEGATIVE 243 117 75 70 11 NC_002967:TDE2413|5end_hypothetical_protein_2440988..2441218_NEGATIVE 242 138 108 56 17 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 239 105 61 227 172 NC_002967:TDE2329|5end_hypothetical_protein_2366493..2366723_NEGATIVE 237 98 54 97 63 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 231 109 61 187 139 NC_002967:TDE1875|5end_hypothetical_protein_1896906..1897136_NEGATIVE 228 132 96 107 69 NC_002967:TDE0575|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_607733..607963_NEGATIVE 227 97 65 85 43 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 104 66 67 29 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 308 126 81 79 35 NC_002967:TDE1115|3end_DNA-binding_protein,_putative_1149038..1149188_NEGATIVE 299 85 44 42 6 NC_002967:TDE1440|3end_glucose-1-phosphate_thymidylyltransferase_1486308..1486458_POSITIVE 244 109 61 103 54 NC_002967:TDE0479|3end_hydroxylamine_reductase_535029..535179_NEGATIVE 237 98 54 127 93 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 229 128 82 104 61 NC_002967:TDE2588|3end_integrase_domain_protein_2624778..2624928_POSITIVE 228 90 44 52 13 NC_002967:TDE2584|3end_dipeptidase_2617944..2618094_POSITIVE 228 112 71 67 28 NC_002967:TDE0904|3end_hypothetical_protein_922278..922428_NEGATIVE 228 132 96 114 76 NC_002967:TDE0576|3end_glutamyl-tRNA(Gln)_amidotransferase,_A_subunit_607726..607876_NEGATIVE 227 140 100 50 9 NC_002967:TDE1771|3end_hypothetical_protein_1814579..1814729_NEGATIVE 226 116 78 144 107 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE 222 91 56 50 12 NC_002967:TDE0340|3end_fructose-bisphosphate_aldolase_379606..379756_POSITIVE 222 77 55 149 128 NC_002967:TDE0024|3end_glycosyl_hydrolase,_family_3_29419..29569_NEGATIVE 221 117 72 108 75 NC_002967:TDE2413|3end_hypothetical_protein_2440323..2440473_NEGATIVE 221 88 61 77 41 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 221 116 73 56 12 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 218 142 104 51 8 NC_002967:TDE2149|3end_transglycosylase,_SLT_family_2185965..2186115_NEGATIVE 216 95 71 29 4 NC_002967:TDE1538|3end_DNA_ligase,_NAD-dependent_1583585..1583735_POSITIVE 213 120 73 150 93 NC_002967:TDE0093|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_112308..112458_POSITIVE 211 104 72 123 96 NC_002967:TDE2784|3end_hypothetical_protein_2838627..2838777_POSITIVE