Origin IGS: actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt .........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 actactactgagtttctgtgcagatgccgaacagcccagtaggagcaggagtataatcgatttgcttgctttattcattttttacgaaatctttcttatttcagcgtccaaagatagcacaccttagcacaaacgaaaagtctatgacccggagcttccgcttggtatttatacacctcaatacagctaattccgaaacggcaatccatttctcgtctattcattatatttttgtgactgttttacattttgaggagacaatcaacacaattaaataactaaaaaagaaagagt Mask Tandem Repeat Region ================================================ actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt Find is-nt database================================================ Query_seq: PG0234:PG0235|PG0234:PG0235:immunoreactive 23 kDa antigen PG66:carboxyl-terminal protease:<-->:271475..271768 294 actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0234:PG0235|PG0234:PG0235:immunoreactive 23 kDa antigen PG66:carboxyl-terminal protease:<-->:271475..271768 294 actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0234:PG0235|PG0234:PG0235:immunoreactive 23 kDa antigen PG66:carboxyl-terminal protease:<-->:271475..271768 294 actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 75 End: 191 .......................................................................... M D E K W I A V S E L A V L R C I N T K R K L R V I D F S F V L R C A I F G R ....................................................................................................... Protein_Len: 43 Strand: + Start: 68 End: 196 ................................................................... M M N R R E M D C R F G I S C I E V Y K Y Q A E A P G H R L F V C A K V C Y L W T L K .................................................................................................. Protein_Len: 39 Strand: - Start: 171 End: 287 .......................................................................................................................................................................... P T S D K S A S I L F I E Y F I F L A L L D I I S R S R S P Q E A D A C F S M ....... Protein_Len: 60 Strand: - Start: 20 End: 235 ................... T V F I Y H I S S F H I A T E S N A T N L H I F V L R F S R T M S K E N T S L H A I K P R Q F L F S K T F F S Y L L C M ........................................................... actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0234:PG0235|PG0234:PG0235:immunoreactive 23 kDa antigen PG66:carboxyl-terminal protease:<-->:271475..271768 294 actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt Intra-Species Hit: Count: 1 Min: 1 Max: 294 Len: 294 Subject: NC_002950_PG0234_PG0235|immunoreactive 23 kDa antigen PG66:carboxyl-terminal protease|NEGATIVE:POSITIVE|[271475,271768]|294 HSP 1 e-value: 1.0E-165 bit: 583.0 Len: 294 Query Start:1 Query End:294 Subject Strand: POSITIVE Subject Start: 1 Subject End: 294 actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt actctttcttttttagttatttaattgtgttgattgtctcctcaaaatgtaaaacagtcacaaaaatataatgaatagacgagaaatggattgccgtttcggaattagctgtattgaggtgtataaataccaagcggaagctccgggtcatagacttttcgtttgtgctaaggtgtgctatctttggacgctgaaataagaaagatttcgtaaaaaatgaataaagcaagcaaatcgattatactcctgctcctactgggctgttcggcatctgcacagaaactcagtagtagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUUUCUUUUUUAGUUAUUUAAUUGUGUUGAUUGUCUCCUCAAAAUGUAAAACAGUCACAAAAAUAUAAUGAAUAGACGAGAAAUGGAUUGCCGUUUCGGAAUUAGCUGUAUUGAGGUGUAUAAAUACCAAGCGGAAGCUCCGGGUCAUAGACUUUUCGUUUGUGCUAAGGUGUGCUAUCUUUGGACGCUGAAAUAAGAAAGAUUUCGUAAAAAAUGAAUAAAGCAAGCAAAUCGAUUAUACUCCUGCUCCUACUGGGCUGUUCGGCAUCUGCACAGAAACUCAGUAGUAGU ..((((((((.....((((((((.(((((((((((((.....(.....)....))))))).....))))))))))).)))..(((((((....)))))))....(((((.((...((((((.....(((((.(((....)))...((.(((((((.....)))))))))..)))))..))))))...)))))))...)))))))).(((((.....)))))...........................(((.((((((((...(((.((....))...))).)))))))).))) (-68.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUACUACUGAGUUUCUGUGCAGAUGCCGAACAGCCCAGUAGGAGCAGGAGUAUAAUCGAUUUGCUUGCUUUAUUCAUUUUUUACGAAAUCUUUCUUAUUUCAGCGUCCAAAGAUAGCACACCUUAGCACAAACGAAAAGUCUAUGACCCGGAGCUUCCGCUUGGUAUUUAUACACCUCAAUACAGCUAAUUCCGAAACGGCAAUCCAUUUCUCGUCUAUUCAUUAUAUUUUUGUGACUGUUUUACAUUUUGAGGAGACAAUCAACACAAUUAAAUAACUAAAAAAGAAAGAGU ....((((((.(((..((.((....))))...))).)))))).((((((...((.....))...))))))...................((((((((.....((((((((((((((.......(((((......((...((.(((((..(.((((....)))).)...))))).)).))......)))))....((((.((....)).))))..............)))))))).))).))).......(((((....)..))))...................)))))))).. (-49.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 140 91 231 182 NC_002950:PG0234|5end_immunoreactive_23_kDa_antigen_PG66_271384..271614_NEGATIVE 400 268 226 46 6 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 393 270 229 77 41 NC_002950:PG0104|5end_DNA_topoisomerase_III_125341..125571_POSITIVE 354 269 244 70 46 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 352 290 250 37 2 NC_002950:PG0127|5end_ferrochelatase_148550..148780_POSITIVE 347 279 235 212 163 NC_002950:PG1080|5end_3-hydroxyacyl-CoA_dehydrogenase_family_protein_1147366..1147596_POSITIVE 347 179 135 99 58 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 345 180 132 229 183 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 345 180 132 84 38 NC_002950:PG0979|5end_hypothetical_protein_1040752..1040982_POSITIVE 344 190 141 194 130 NC_002950:PG0678|5end_pyrazinamidase/nicotinamidase,_putative_728879..729109_POSITIVE 338 209 161 198 140 NC_002950:PG1872|5end_urocanate_hydratase_1968911..1969141_NEGATIVE 336 285 248 161 116 NC_002950:PG0739|5end_ribonuclease_Z_786947..787177_POSITIVE 334 286 241 161 112 NC_002950:PG1715|5end_hypothetical_protein_1806056..1806286_NEGATIVE 334 179 132 229 191 NC_002950:PG0489|5end_polysaccharide_biosynthesis-related_protein_529247..529477_POSITIVE 332 275 245 71 33 NC_002950:PG1755|5end_fructose-bisphosphate_aldolase_1843278..1843508_NEGATIVE 330 187 143 219 175 NC_002950:PG0445|5end_peptidase_T_485252..485482_POSITIVE 330 150 101 51 5 NC_002950:PG0316|5end_seryl-tRNA_synthetase_348437..348667_POSITIVE 329 183 141 225 185 NC_002950:PG0558|5end_purine_nucleoside_phosphorylase_616331..616561_NEGATIVE 326 272 239 119 84 NC_002950:PG0212|5end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_249065..249295_NEGATIVE 324 178 131 61 10 NC_002950:PG0155|5end_riboflavin_biosynthesis_protein_RibD_178853..179083_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 280 234 143 86 NC_002950:PG1030|3end_hypothetical_protein_1092820..1092970_POSITIVE 354 269 244 57 33 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 345 180 132 114 68 NC_002950:PG0978|3end_shikimate_5-dehydrogenase_1040862..1041012_POSITIVE 341 179 136 140 88 NC_002950:PG0677|3end_saccharopine_dehydrogenase_728926..729076_POSITIVE 338 276 246 148 116 NC_002950:PG0384|3end_MutS2_family_protein_418697..418847_POSITIVE 337 170 121 146 99 NC_002950:PG0245|3end_universal_stress_protein_family_279773..279923_NEGATIVE 336 272 245 92 65 NC_002950:PG1745|3end_phosphoribulokinase_family_protein_1829435..1829585_NEGATIVE 336 285 248 129 84 NC_002950:PG0738|3end_cytidine/deoxycytidylate_deaminase_family_protein_786995..787145_POSITIVE 334 279 246 35 1 NC_002950:PG0327|3end_hypothetical_protein_360907..361057_NEGATIVE 326 272 239 126 91 NC_002950:PG0213|3end_precorrin-3_methylase/precorrin-8X_methylmutase_249058..249208_NEGATIVE 324 285 248 47 5 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 323 269 225 53 3 NC_002950:PG2204|3end_hypothetical_protein_2316187..2316337_POSITIVE 321 288 244 95 51 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 318 189 141 121 80 NC_002950:PG0756|3end_hypothetical_protein_804321..804471_NEGATIVE 317 275 248 64 30 NC_002950:PG0632|3end_biopolymer_transport_protein_ExbD,_putative_685376..685526_POSITIVE 311 285 248 63 21 NC_002950:PG1355|3end_acyltransferase,_putative_1434762..1434912_NEGATIVE 310 122 82 105 49 NC_002950:PG1081|3end_acetate_kinase_1148431..1148581_NEGATIVE 308 177 131 142 80 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 307 168 129 149 103 NC_002950:PG0140|3end_hypothetical_protein_163151..163301_NEGATIVE 304 178 133 150 93 NC_002950:PG2069|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2165609..2165759_POSITIVE