Origin IGS: aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat .........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 atattgtcaaagctaagtttctgctgttcaaaggtaatcaaataatcccctgcttcacgtattcggctgttcgggtctcgtctgaaaaacatttttgtaattttttgaaacactcttcagacacacattttcaggtgaaaattgtcaatttttgctcttgcactcgtaactgattgaaataatggctgttaacggtttttcatgcgtgatttgtccaaattgcaccttaattcgttagtttttttgtacacaaatgcgtgatttgtccaagaaaatgcgtgatttgtccaagtcttttccttaatatatcccttcatttgtgtgactcttaaagtgtaagagcctaaagtcacagttttaatcaatctaaaatttttcaatt Mask Tandem Repeat Region ================================================ aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat Find is-nt database================================================ Query_seq: PG1055:PG1056|PG1055:PG1056:thiol protease:hypothetical protein:<-->:1122738..1123119 382 aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1055:PG1056|PG1055:PG1056:thiol protease:hypothetical protein:<-->:1122738..1123119 382 aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1055:PG1056|PG1055:PG1056:thiol protease:hypothetical protein:<-->:1122738..1123119 382 aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 3 End: 191 .. M K N F R L I K T V T L G S Y T L R V T Q M K G Y I K E K T W T N H A F S W T N H A F V Y K K T N E L R C N L D K S R M ............................................................................................................................................................................................... Protein_Len: 37 Strand: + Start: 270 End: 380 ............................................................................................................................................................................................................................................................................. M F Q K I T K M F F R R D P N S R I R E A G D Y L I T F E Q Q K L S F D N .. Protein_Len: 56 Strand: - Start: 213 End: 380 .................................................................................................................................................................................................................... N R T C S C F N V I K V Q F H T D S S H K L F N C F H K E S S V R V A S Y T F C P I I Q N G K F L L F K A K V M .. aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat 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================================================ aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1055:PG1056|PG1055:PG1056:thiol protease:hypothetical protein:<-->:1122738..1123119 382 aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat Intra-Species Hit: Count: 1 Min: 1 Max: 382 Len: 382 Subject: NC_002950_PG1055_PG1056|thiol protease:hypothetical protein|NEGATIVE:POSITIVE|[1122738,1123119]|382 HSP 1 e-value: 0.0 bit: 716.0 Len: 382 Query Start:1 Query End:382 Subject Strand: POSITIVE Subject Start: 1 Subject End: 382 aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacnnnnnnnctaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat aattgaaaaattttagattgattaaaactgtgactttaggctcttacactttaagagtcacacaaatgaagggatatattaaggaaaagacttggacaaatcacgcattttcttggacaaatcacgcatttgtgtacaaaaaaactaacgaattaaggtgcaatttggacaaatcacgcatgaaaaaccgttaacagccattatttcaatcagttacgagtgcaagagcaaaaattgacaattttcacctgaaaatgtgtgtctgaagagtgtttcaaaaaattacaaaaatgtttttcagacgagacccgaacagccgaatacgtgaagcaggggattatttgattacctttgaacagcagaaacttagctttgacaatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUGAAAAAUUUUAGAUUGAUUAAAACUGUGACUUUAGGCUCUUACACUUUAAGAGUCACACAAAUGAAGGGAUAUAUUAAGGAAAAGACUUGGACAAAUCACGCAUUUUCUUGGACAAAUCACGCAUUUGUGUACAAAAAAACUAACGAAUUAAGGUGCAAUUUGGACAAAUCACGCAUGAAAAACCGUUAACAGCCAUUAUUUCAAUCAGUUACGAGUGCAAGAGCAAAAAUUGACAAUUUUCACCUGAAAAUGUGUGUCUGAAGAGUGUUUCAAAAAAUUACAAAAAUGUUUUUCAGACGAGACCCGAACAGCCGAAUACGUGAAGCAGGGGAUUAUUUGAUUACCUUUGAACAGCAGAAACUUAGCUUUGACAAUAU .((((......((((((.((((((((..(((.(.(((..((((((.(((((.....((.(((((((((....(((......(((((((..(.(((.....))).)..)))))))......)))...))))))))))).....((((...(((.((((((......(((.....(((....)))....)))......))).))).)))....))))..))))).))))))..))).).)))...(((.((((...((((((((((((((((..(((.............)))..))))))))))......((......)).))))))....)))))))...))))))))..)))))).(((.........)))....)))).. (-76.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUGUCAAAGCUAAGUUUCUGCUGUUCAAAGGUAAUCAAAUAAUCCCCUGCUUCACGUAUUCGGCUGUUCGGGUCUCGUCUGAAAAACAUUUUUGUAAUUUUUUGAAACACUCUUCAGACACACAUUUUCAGGUGAAAAUUGUCAAUUUUUGCUCUUGCACUCGUAACUGAUUGAAAUAAUGGCUGUUAACGGUUUUUCAUGCGUGAUUUGUCCAAAUUGCACCUUAAUUCGUUAGUUUUUUUGUACACAAAUGCGUGAUUUGUCCAAGAAAAUGCGUGAUUUGUCCAAGUCUUUUCCUUAAUAUAUCCCUUCAUUUGUGUGACUCUUAAAGUGUAAGAGCCUAAAGUCACAGUUUUAAUCAAUCUAAAAUUUUUCAAUU ....((((..(((.........))).((((((((...(((.((...(((..((..(.((....)))..))..)))....)).)))...(((....)))...))))))))..........))))..........(((.((((((((...(((..(((((((((((...((((((((((((....(((((....))))))))))...(..((((....))))..)..........)))))))......((((((((((.(.(((.(((....(((((.((.((.......)).)).)))))....))).))).)..))))))))))........)))))))))))..)))...)))))))).)))................... (-73.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 130 81 221 172 NC_002950:PG1055|5end_thiol_protease_1122647..1122877_NEGATIVE 654 130 82 92 43 NC_002950:PG2103|5end_hypothetical_protein_2213360..2213590_NEGATIVE 360 342 308 62 19 NC_002950:PG0611|5end_lipoprotein,_putative_664012..664242_POSITIVE 330 341 301 191 145 NC_002950:PG2143|5end_GTP-binding_protein_EngA_2248547..2248777_POSITIVE 321 350 304 88 41 NC_002950:PG1176|5end_ABC_transporter,_ATP-binding_protein,_putative_1257644..1257874_NEGATIVE 302 338 299 44 1 NC_002950:PG1978|5end_hypothetical_protein_2067337..2067567_NEGATIVE 301 335 308 221 180 NC_002950:PG1659|5end_hypothetical_protein_1743747..1743977_NEGATIVE 300 336 293 142 103 NC_002950:PG0235|5end_carboxyl-terminal_protease_271629..271859_POSITIVE 300 336 299 50 10 NC_002950:PG0083|5end_hypothetical_protein_96952..97182_POSITIVE 299 334 292 208 156 NC_002950:PG2180|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_C_2288546..2288776_NEGATIVE 298 331 303 41 8 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 296 349 302 229 179 NC_002950:PG0074|5end_peptide_chain_release_factor_1_89172..89402_NEGATIVE 292 339 295 76 36 NC_002950:PG1044|5end_iron_dependent_repressor,_putative_1113818..1114048_NEGATIVE 292 337 295 95 45 NC_002950:PG0569|5end_hypothetical_protein_626223..626453_NEGATIVE 290 350 303 49 1 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 288 336 291 221 175 NC_002950:PG1556|5end_hypothetical_protein_1636595..1636825_POSITIVE 288 345 308 189 152 NC_002950:PG0523|5end_inositol-5-monophosphate_dehydrogenase_568394..568624_NEGATIVE 287 332 294 228 180 NC_002950:PG0725|5end_hydrolase,_haloacid_dehalogenase-like_family_777260..777490_POSITIVE 284 336 302 229 197 NC_002950:PG0732|5end_hypothetical_protein_782621..782851_POSITIVE 282 335 299 83 52 NC_002950:PG1301|5end_hypothetical_protein_1379921..1380151_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 276 244 91 58 NC_002950:PG1105|3end_RNA_polymerase_sigma-54_factor_1175716..1175866_NEGATIVE 330 341 301 128 82 NC_002950:PG2142|3end_GTP-binding_protein_Era_2248564..2248714_POSITIVE 317 344 303 97 44 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 300 336 299 44 4 NC_002950:PG0082|3end_hypothetical_protein_97026..97176_POSITIVE 291 337 291 76 24 NC_002950:PG0085|3end_alpha-galactosidase_100556..100706_POSITIVE 287 337 304 121 73 NC_002950:PG1789|3end_peptidyl-dipeptidase_Dcp_1877417..1877567_NEGATIVE 287 332 294 143 95 NC_002950:PG0724|3end_prolyl_oligopeptidase_family_protein_777255..777405_POSITIVE 282 335 299 65 34 NC_002950:PG1302|3end_hypothetical_protein_1379939..1380089_NEGATIVE 280 335 291 131 84 NC_002950:PG0926|3end_hypothetical_protein_984407..984557_NEGATIVE 274 337 300 68 28 NC_002950:PG1885|3end_polyphosphate_kinase_1981065..1981215_NEGATIVE 273 338 292 147 83 NC_002950:PG2095|3end_lipoprotein,_putative_2198290..2198440_NEGATIVE 272 338 291 144 94 NC_002950:PG1561|3end_dTDP-4-dehydrorhamnose_reductase_1640138..1640288_NEGATIVE 270 363 323 54 11 NC_002950:PG1498|3end_hypothetical_protein_1575650..1575800_POSITIVE 269 337 291 82 20 NC_002950:PG1732|3end_integrase/recombinase_XerD_1821177..1821327_POSITIVE 269 335 299 146 109 NC_002950:PG0936|3end_xanthine/uracil_permease_family_protein_995150..995300_NEGATIVE 269 337 297 128 90 NC_002950:PG0795|3end_hypothetical_protein_849603..849753_POSITIVE 268 335 300 74 28 NC_002950:PG1186|3end_hypothetical_protein_1267703..1267853_NEGATIVE 265 336 294 127 87 NC_002950:PG1799|3end_hypothetical_protein_1894788..1894938_POSITIVE 263 344 303 149 105 NC_002950:PG1823|3end_hypothetical_protein_1918050..1918200_POSITIVE 263 337 291 52 5 NC_002950:PG0277|3end_ISPg2,_transposase_310066..310216_POSITIVE