Origin IGS: ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataaaattccaattttccttttaatgaaaggggcttataaaatataaagaaagtatatcaaaattttaagataaagaaaagaggagatgaaaccttttaaaaaccacccaatccaattaaaacctcatgtaagtagacagaacatacattataggaagttttataaagggtttttatgagtttttttagaaggaatttttacccattcttcacaataaaatccaagttgacatctctacggcccaacttatccatttataaaatatattctctattttagtcgagtcaacacatattgtgtttattaagatgtattattatttctacaatatttaataattcagtataaaaatgtatacatgttaagattttat Mask Tandem Repeat Region ================================================ ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt Find is-nt database================================================ Query_seq: TDE1576:TDE1577|TDE1576:TDE1577:tRNA-i(6)A37 modification enzyme MiaB:lipoprotein, putative:->->:1624274..1624648 375 ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1576:TDE1577|TDE1576:TDE1577:tRNA-i(6)A37 modification enzyme MiaB:lipoprotein, putative:->->:1624274..1624648 375 ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1576:TDE1577|TDE1576:TDE1577:tRNA-i(6)A37 modification enzyme MiaB:lipoprotein, putative:->->:1624274..1624648 375 ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 64 End: 162 ............................................................... M L I N T I C V D S T K I E N I F Y K W I S W A V E M S T W I L L ..................................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 199 End: 288 ...................................................................................................................................................................................................... L F G K Y F K R Y H I N Q R S V H P K L Q I P H N K F P K M ....................................................................................... Protein_Len: 34 Strand: - Start: 98 End: 199 ................................................................................................. F L S Y I K Y I S L N P R L S T L K S K I T F F P Y F N R R F F S M ................................................................................................................................................................................ ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt 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: 82 Start: 305 End: 334 ................................................................................................................................................................................................................................................................................................................CTTAAAATTTTGATATACTTTCTTTATATT......................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 283 End: 312 ..........................................................................................................................................................................................................................................................................................TTTCATCTCCTCTTTTCTTTATCTTAAAAT............................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1576:TDE1577|TDE1576:TDE1577:tRNA-i(6)A37 modification enzyme MiaB:lipoprotein, putative:->->:1624274..1624648 375 ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt Intra-Species Hit: Count: 1 Min: 1 Max: 375 Len: 375 Subject: NC_002967_TDE1576_TDE1577|tRNA-i(6)A37 modification enzyme MiaB:lipoprotein, putative|POSITIVE:POSITIVE|[1624274,1624648]|375 HSP 1 e-value: 0.0 bit: 702.0 Len: 375 Query Start:1 Query End:375 Subject Strand: POSITIVE Subject Start: 1 Subject End: 375 ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctnnnnnnnctcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt ataaaatcttaacatgtatacatttttatactgaattattaaatattgtagaaataataatacatcttaataaacacaatatgtgttgactcgactaaaatagagaatatattttataaatggataagttgggccgtagagatgtcaacttggattttattgtgaagaatgggtaaaaattccttctaaaaaaactcataaaaaccctttataaaacttcctataatgtatgttctgtctacttacatgaggttttaattggattgggtggtttttaaaaggtttcatctcctcttttctttatcttaaaattttgatatactttctttatattttataagcccctttcattaaaaggaaaattggaattttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAUCUUAACAUGUAUACAUUUUUAUACUGAAUUAUUAAAUAUUGUAGAAAUAAUAAUACAUCUUAAUAAACACAAUAUGUGUUGACUCGACUAAAAUAGAGAAUAUAUUUUAUAAAUGGAUAAGUUGGGCCGUAGAGAUGUCAACUUGGAUUUUAUUGUGAAGAAUGGGUAAAAAUUCCUUCUAAAAAAACUCAUAAAAACCCUUUAUAAAACUUCCUAUAAUGUAUGUUCUGUCUACUUACAUGAGGUUUUAAUUGGAUUGGGUGGUUUUUAAAAGGUUUCAUCUCCUCUUUUCUUUAUCUUAAAAUUUUGAUAUACUUUCUUUAUAUUUUAUAAGCCCCUUUCAUUAAAAGGAAAAUUGGAAUUUUAUU (((((((((......((..((((((((((.(..(.(((((.....((((((((...................(((((.....)))))..(((..........)))......))))))))...))))).)..)...))))))))))..))..))))))))).((((((((.(((........((((.((((((.(((((.......((....(((((((((.....(((((.((.......)).))))))))))))))...))..)))))..)))))).))))........)))...))))))))..((((((((..((........((((((...))))))..(((((.....)))))...))..)))))))).. (-68.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAAUUCCAAUUUUCCUUUUAAUGAAAGGGGCUUAUAAAAUAUAAAGAAAGUAUAUCAAAAUUUUAAGAUAAAGAAAAGAGGAGAUGAAACCUUUUAAAAACCACCCAAUCCAAUUAAAACCUCAUGUAAGUAGACAGAACAUACAUUAUAGGAAGUUUUAUAAAGGGUUUUUAUGAGUUUUUUUAGAAGGAAUUUUUACCCAUUCUUCACAAUAAAAUCCAAGUUGACAUCUCUACGGCCCAACUUAUCCAUUUAUAAAAUAUAUUCUCUAUUUUAGUCGAGUCAACACAUAUUGUGUUUAUUAAGAUGUAUUAUUAUUUCUACAAUAUUUAAUAAUUCAGUAUAAAAAUGUAUACAUGUUAAGAUUUUAU .((((((((.......(((((((....))))))).((((.((((((..((((((((((((......((((((((.((((....(((((((...((((((((((((((...(((((...((((((.((.((((((((.........))).))))).)).))))))....)))))....)).))..))))))))))...................((((.........)))).)))))))..((..........))..............)))).))))))))...(((.(((((.....))))).)))..))))))).....)))))...)))))).))))....(((((......))))).......)))))))) (-61.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 172 131 219 181 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 299 356 312 131 79 NC_002967:TDE0284|5end_hypothetical_protein_313428..313658_NEGATIVE 296 256 214 188 136 NC_002967:TDE0897|5end_ABC_transporter,_ATP-binding/permease_protein_914113..914343_POSITIVE 281 178 132 165 112 NC_002967:TDE1681|5end_V-type_ATP_synthase_subunit_D_1733537..1733767_NEGATIVE 265 290 241 72 19 NC_002967:TDE1913|5end_hypothetical_protein_1929810..1930040_POSITIVE 262 327 281 216 176 NC_002967:TDE0383|5end_hypothetical_protein_434609..434839_POSITIVE 259 154 119 124 95 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 254 269 230 38 1 NC_002967:TDE1198|5end_S-adenosyl-methyltransferase_MraW_1230392..1230622_POSITIVE 250 164 124 186 144 NC_002967:TDE2063|5end_ferrous_iron_transport_protein_B_2091264..2091494_NEGATIVE 247 321 284 217 182 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 245 252 213 66 26 NC_002967:TDE0717|5end_hypothetical_protein_751779..752009_POSITIVE 240 126 84 218 177 NC_002967:TDE1089|5end_hypothetical_protein_1120944..1121174_NEGATIVE 240 169 122 211 158 NC_002967:TDE0213|5end_TPR_domain_protein_249460..249690_NEGATIVE 235 302 261 198 146 NC_002967:TDE0604|5end_hypothetical_protein_642631..642861_NEGATIVE 233 308 261 214 149 NC_002967:TDE1104|5end_tRNA_pseudouridine_synthase_B_1137786..1138016_NEGATIVE 233 158 118 205 165 NC_002967:TDE0845|5end_conserved_hypothetical_protein_TIGR00266_867795..868025_POSITIVE 232 271 233 162 124 NC_002967:TDE2441|5end_hypothetical_protein_2472496..2472726_NEGATIVE 227 255 228 188 159 NC_002967:TDE2757|5end_nucleotidyltransferase_family_protein_2813673..2813903_POSITIVE 227 281 249 42 4 NC_002967:TDE2448|5end_hypothetical_protein_2477417..2477647_NEGATIVE 225 170 127 173 136 NC_002967:TDE2696|5end_TPR_domain_protein_2740036..2740266_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 268 221 102 58 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 266 168 133 88 52 NC_002967:TDE2110|3end_orotidine_5'-phosphate_decarboxylase_2136311..2136461_POSITIVE 265 290 241 70 17 NC_002967:TDE1912|3end_redox-sensing_transcriptional_repressor_Rex_1929888..1930038_POSITIVE 254 175 132 151 101 NC_002967:TDE1682|3end_V-type_ATP_synthase_subunit_B_1733548..1733698_NEGATIVE 242 296 251 85 34 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 236 269 222 116 63 NC_002967:TDE2490|3end_primosomal_protein_N'_2512703..2512853_NEGATIVE 236 177 132 85 29 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE 233 158 118 103 63 NC_002967:TDE0844|3end_pyruvate_phosphate_dikinase,_putative_867773..867923_POSITIVE 232 270 221 111 71 NC_002967:TDE1753|3end_UDP-glucose_4-epimerase_1805521..1805671_NEGATIVE 231 175 131 106 67 NC_002967:TDE2724|3end_hypothetical_protein_2782282..2782432_POSITIVE 231 302 265 109 72 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 226 165 128 107 69 NC_002967:TDE2206|3end_hypothetical_protein_2244921..2245071_NEGATIVE 226 293 261 118 73 NC_002967:TDE1630|3end_hypothetical_protein_1678642..1678792_NEGATIVE 225 177 132 105 38 NC_002967:TDE2328|3end_efflux_pump_component_MtrF_2366364..2366514_POSITIVE 225 190 143 139 97 NC_002967:TDE0003|3end_hypothetical_protein_4282..4432_POSITIVE 224 300 251 70 23 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 224 308 265 52 8 NC_002967:TDE0026|3end_TraB_family_protein_31826..31976_NEGATIVE 221 168 127 79 34 NC_002967:TDE2656|3end_cobalt_chelatase_2693900..2694050_POSITIVE 221 272 231 118 74 NC_002967:TDE1031|3end_hypothetical_protein_1060185..1060335_POSITIVE 219 239 207 109 76 NC_002967:TDE0631|3end_sigma_factor_regulatory_protein,_putative_667501..667651_POSITIVE