Origin IGS: ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac .........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 gtcttcaggagcaacaaatgcaaaaattttggcacgtaaacaggcccaacggagatgatgcccgggcttttttaatagcagtttgtatagggcattgtattagccataagcatagctcctgagtcattcccataaagacgggcagttaaaatccgatcacctccccatatccactcattatttgtacgtaaatgtcttttttcagactttaaatacttatatttatcccgaaaaattacccaagagagattgggtcgattgtcgatccgtcttaagtcatacaatccaataatcattattgaa Mask Tandem Repeat Region ================================================ ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac Find is-nt database================================================ Query_seq: PG1798:PG1799|PG1798:PG1799:immunoreactive 46 kDa antigen PG99:hypothetical protein:<-->:1894336..1894638 303 ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1798:PG1799|PG1798:PG1799:immunoreactive 46 kDa antigen PG99:hypothetical protein:<-->:1894336..1894638 303 ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1798:PG1799|PG1798:PG1799:immunoreactive 46 kDa antigen PG99:hypothetical protein:<-->:1894336..1894638 303 ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 5 End: 229 .... M M I I G L Y D L R R I D N R P N L S W V I F R D K Y K Y L K S E K R H L R T N N E W I W G G D R I L T A R L Y G N D S .......................................................................... Protein_Len: 46 Strand: + Start: 159 End: 296 .............................................................................................................................................................. M P V F M G M T Q E L C L W L I Q C P I Q T A I K K A R A S S P L G L F T C Q N F C I C C S ....... Protein_Len: 34 Strand: - Start: 185 End: 286 ........................................................................................................................................................................................ S S H K H S I C H G I C V A I L F A R A D D G N P R N V H W F K Q M ................. Protein_Len: 57 Strand: - Start: 15 End: 185 .............. Q I T H S L V S R C D V W D R K P L K E P Y I Y T N L T Q F F V N V Y L Y H T S I P L H D S K L Q G D K H S H S M ...................................................................................................................... Protein_Len: 51 Strand: - Start: 1 End: 153 E I I I I P N Y S K L R I S L R G L R E Q T I K R S L Y L Y K F D S F L C K R V F L S H I H P P S R M ...................................................................................................................................................... ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac 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================================================ ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -2.1 Tail_Score: -3.35542 Start: 48 End: 67 Full_Region: GACGGATCGACAATC GACCCAA TCTCTC TTGGGTA ATTTTTCGGGATAAA ...............................................GACCCAATCTCTCTTGGGTA............................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 54 HP_score: -4.7 Tail_Score: -3.24422 Start: 50 End: 65 Full_Region: CGGATCGACAATCGA CCCAA TCTCTC TTGGG TAATTTTTCGGGATA .................................................CCCAATCTCTCTTGGG.............................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 49 HP_score: -4.7 Tail_Score: -2.6063 Start: 50 End: 65 Full_Region: tatcccgaaaaatta cccaa gagaga ttggg tcgattgtcgatccg .................................................cccaagagagattggg.............................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: PG1798:PG1799|PG1798:PG1799:immunoreactive 46 kDa antigen PG99:hypothetical protein:<-->:1894336..1894638 303 ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac Intra-Species Hit: Count: 1 Min: 1 Max: 303 Len: 303 Subject: NC_002950_PG1798_PG1799|immunoreactive 46 kDa antigen PG99:hypothetical protein|NEGATIVE:POSITIVE|[1894336,1894638]|303 HSP 1 e-value: 1.0E-171 bit: 601.0 Len: 303 Query Start:1 Query End:303 Subject Strand: POSITIVE Subject Start: 1 Subject End: 303 ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac ttcaataatgattattggattgtatgacttaagacggatcgacaatcgacccaatctctcttgggtaatttttcgggataaatataagtatttaaagtctgaaaaaagacatttacgtacaaataatgagtggatatggggaggtgatcggattttaactgcccgtctttatgggaatgactcaggagctatgcttatggctaatacaatgccctatacaaactgctattaaaaaagcccgggcatcatctccgttgggcctgtttacgtgccaaaatttttgcatttgttgctcctgaagac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAUAAUGAUUAUUGGAUUGUAUGACUUAAGACGGAUCGACAAUCGACCCAAUCUCUCUUGGGUAAUUUUUCGGGAUAAAUAUAAGUAUUUAAAGUCUGAAAAAAGACAUUUACGUACAAAUAAUGAGUGGAUAUGGGGAGGUGAUCGGAUUUUAACUGCCCGUCUUUAUGGGAAUGACUCAGGAGCUAUGCUUAUGGCUAAUACAAUGCCCUAUACAAACUGCUAUUAAAAAAGCCCGGGCAUCAUCUCCGUUGGGCCUGUUUACGUGCCAAAAUUUUUGCAUUUGUUGCUCCUGAAGAC ..(((((.....)))))((((((.(((((......)).))))))))).((((((......))))))...(((((((((.........((((.((((((((......)))).)))).))))...(((..((((.......((((((((............((((((....((((((.((........((((((....))))))......))..))))))......(((........))).))))))))))))))....(((.((....)).)))..........))))..))).))))))))). (-76.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUUCAGGAGCAACAAAUGCAAAAAUUUUGGCACGUAAACAGGCCCAACGGAGAUGAUGCCCGGGCUUUUUUAAUAGCAGUUUGUAUAGGGCAUUGUAUUAGCCAUAAGCAUAGCUCCUGAGUCAUUCCCAUAAAGACGGGCAGUUAAAAUCCGAUCACCUCCCCAUAUCCACUCAUUAUUUGUACGUAAAUGUCUUUUUUCAGACUUUAAAUACUUAUAUUUAUCCCGAAAAAUUACCCAAGAGAGAUUGGGUCGAUUGUCGAUCCGUCUUAAGUCAUACAAUCCAAUAAUCAUUAUUGAA ...(((((((((.....(((((((.......((...((((.((((((...((........)).)))))).))))...))..)))))))..(((.........))).........)))))))))...........((((((((....................................(((..(((..((((.((((......))))))))..)))..))).......(((..((((((((((......)))))).)))).))).)))))))).............(((((.....))))).. (-67.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 920 80 31 171 122 NC_002950:PG1798|5end_immunoreactive_46_kDa_antigen_PG99_1894245..1894475_NEGATIVE 401 274 232 90 32 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 368 176 136 61 2 NC_002950:PG0992|5end_threonyl-tRNA_synthetase_1054104..1054334_NEGATIVE 357 274 236 231 186 NC_002950:PG0290|5end_hypothetical_protein_323904..324134_POSITIVE 346 165 126 221 173 NC_002950:PG0125|5end_hypothetical_protein_146786..147016_NEGATIVE 338 298 254 40 1 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 336 189 141 190 130 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 332 269 235 169 135 NC_002950:PG2097|5end_ribose-phosphate_pyrophosphokinase_2206462..2206692_NEGATIVE 331 274 237 154 121 NC_002950:PG0636|5end_MATE_efflux_family_protein_689071..689301_NEGATIVE 328 200 160 84 45 NC_002950:PG0908|5end_G/U_mismatch-specific_DNA_glycosylase,_putative_971721..971951_NEGATIVE 327 276 239 190 142 NC_002950:PG1310|5end_exsB_protein_1389084..1389314_POSITIVE 327 269 223 221 178 NC_002950:PG0149|5end_hypothetical_protein_172203..172433_NEGATIVE 323 273 235 211 156 NC_002950:PG0364|5end_hypothetical_protein_399615..399845_NEGATIVE 321 168 128 183 144 NC_002950:PG0615|5end_GTP-binding_protein_TypA_667033..667263_POSITIVE 319 276 237 214 170 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 319 262 222 44 2 NC_002950:PG0034|5end_thioredoxin_42549..42779_NEGATIVE 318 300 251 222 169 NC_002950:PG2205|5end_2-dehydropantoate_2-reductase_2316121..2316351_POSITIVE 317 269 221 118 50 NC_002950:PG0337|5end_hypothetical_protein_371529..371759_NEGATIVE 312 300 251 185 141 NC_002950:PG1659|5end_hypothetical_protein_1743747..1743977_NEGATIVE 311 189 141 76 5 NC_002950:PG1164|5end_hypothetical_protein_1247514..1247744_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 274 232 83 25 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 395 296 251 136 96 NC_002950:PG1655|3end_hypothetical_protein_1737384..1737534_POSITIVE 345 169 127 56 6 NC_002950:PG1742|3end_hypothetical_protein_1827506..1827656_POSITIVE 328 200 160 67 28 NC_002950:PG0909|3end_hypothetical_protein_971738..971888_NEGATIVE 311 189 141 79 8 NC_002950:PG1165|3end_hypothetical_protein_1247511..1247661_NEGATIVE 310 262 225 77 36 NC_002950:PG1361|3end_dipeptidyl_aminopeptidase_IV,_putative_1439910..1440060_NEGATIVE 310 298 253 132 79 NC_002950:PG0594|3end_RNA_polymerase_sigma-70_factor_652991..653141_POSITIVE 308 273 236 50 15 NC_002950:PG0317|3end_peptidase,_M49_family_349771..349921_NEGATIVE 306 189 142 46 1 NC_002950:PG0017|3end_sensor_histidine_kinase_19724..19874_POSITIVE 301 202 161 72 21 NC_002950:PG1755|3end_fructose-bisphosphate_aldolase_1842397..1842547_NEGATIVE 298 199 151 62 15 NC_002950:PG1864|3end_leucine-rich_protein_1960509..1960659_NEGATIVE 298 275 231 86 32 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 297 186 141 146 94 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 295 203 163 145 104 NC_002950:PG1922|3end_ribosomal_protein_L18_2017027..2017177_NEGATIVE 295 260 211 138 81 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 290 261 221 145 97 NC_002950:PG1375|3end_hypothetical_protein_1456743..1456893_POSITIVE 289 269 224 77 30 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 289 202 161 103 51 NC_002950:PG0246|3end_hypothetical_protein_281050..281200_NEGATIVE 288 273 233 83 35 NC_002950:PG0770|3end_hypothetical_protein_824159..824309_NEGATIVE 287 270 239 55 21 NC_002950:PG1760|3end_ABC_transporter,_ATP-binding_protein_1847216..1847366_POSITIVE