Origin IGS: agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat .........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 atcgtttacgtgtgcaacacactttccttctgctgcaacagcttctatttcaaccttttctaatataggtaacggtttccttttcctgctcattctcttatatttgctgcaaagttagttattttttttggtttgcatagcagccttgtgctaaaactgctgatactgctctactattccaaacaacgttacttatcaattaaaacgaagttgtaaaaacctctaaaagcactatacatattatatataacaagcttttatggttgttttcaatagtgtttaatgataaaaagttaagaattgtttttgttttctattaaatattattatctttgctgcgtaagacagtaaactcagtagaatatttaaaagagatttatgaaaaagtttttcatagtggcagct Mask Tandem Repeat Region ================================================ agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat Find is-nt database================================================ Query_seq: PI1089:PI1090|PI1089:PI1090:conserved hypothetical protein:tRNA uracil 5-methyltransferase:->->:1014101..1014505 405 agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1089:PI1090|PI1089:PI1090:conserved hypothetical protein:tRNA uracil 5-methyltransferase:->->:1014101..1014505 405 agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1089:PI1090|PI1089:PI1090:conserved hypothetical protein:tRNA uracil 5-methyltransferase:->->:1014101..1014505 405 agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 105 End: 203 ........................................................................................................ M L N F L S L N T I E N N H K S L L Y I I C I V L L E V F T T S F .......................................................................................................................................................................................................... Protein_Len: 31 Strand: + Start: 313 End: 405 ........................................................................................................................................................................................................................................................................................................................ M S R K R K P L P I L E K V E I E A V A A E G K C V A H V N D Protein_Len: 38 Strand: - Start: 193 End: 306 ................................................................................................................................................................................................ L K T K I S L Y R Q K S Y Y L L I L L K L V L S S H L G F F I V L K A A F M ................................................................................................... agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat 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: 81 Start: 302 End: 331 .............................................................................................................................................................................................................................................................................................................GTTTCCTTTTCCTGCTCATTCTCTTATATT.......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -3.0 Tail_Score: -3.26844 Start: 183 End: 199 Full_Region: TGTATAGTGCTTTTA GAGGTT TTTAC AACTTC GTTTTAATTGATAAG ......................................................................................................................................................................................GAGGTTTTTACAACTTC.............................................................................................................................................................................................................. Find igs database================================================ Query_seq: PI1089:PI1090|PI1089:PI1090:conserved hypothetical protein:tRNA uracil 5-methyltransferase:->->:1014101..1014505 405 agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat Intra-Species Hit: Count: 1 Min: 1 Max: 405 Len: 405 Subject: pint_PI1089_PI1090|conserved hypothetical protein:tRNA uracil 5-methyltransferase|POSITIVE:POSITIVE|[1014101, 1014505]|405 HSP 1 e-value: 0.0 bit: 755.0 Len: 405 Query Start:1 Query End:405 Subject Strand: POSITIVE Subject Start: 1 Subject End: 405 agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccnnnnnnnntaactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat agctgccactatgaaaaactttttcataaatctcttttaaatattctactgagtttactgtcttacgcagcaaagataataatatttaatagaaaacaaaaacaattcttaactttttatcattaaacactattgaaaacaaccataaaagcttgttatatataatatgtatagtgcttttagaggtttttacaacttcgttttaattgataagtaacgttgtttggaatagtagagcagtatcagcagttttagcacaaggctgctatgcaaaccaaaaaaaataactaactttgcagcaaatataagagaatgagcaggaaaaggaaaccgttacctatattagaaaaggttgaaatagaagctgttgcagcagaaggaaagtgtgttgcacacgtaaacgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGCCACUAUGAAAAACUUUUUCAUAAAUCUCUUUUAAAUAUUCUACUGAGUUUACUGUCUUACGCAGCAAAGAUAAUAAUAUUUAAUAGAAAACAAAAACAAUUCUUAACUUUUUAUCAUUAAACACUAUUGAAAACAACCAUAAAAGCUUGUUAUAUAUAAUAUGUAUAGUGCUUUUAGAGGUUUUUACAACUUCGUUUUAAUUGAUAAGUAACGUUGUUUGGAAUAGUAGAGCAGUAUCAGCAGUUUUAGCACAAGGCUGCUAUGCAAACCAAAAAAAAUAACUAACUUUGCAGCAAAUAUAAGAGAAUGAGCAGGAAAAGGAAACCGUUACCUAUAUUAGAAAAGGUUGAAAUAGAAGCUGUUGCAGCAGAAGGAAAGUGUGUUGCACACGUAAACGAU ..((((..((((....(((((((((.....((((((.((.......(((((..((((((((..((.(((((..(((((....)))))............................(((((((..((((....(((.(((.((((.(((((((...((((((((...)))))))).)))))))..))))))).)))....))))....)))))))....))))).))..)))))))).)))))..(((((((((.....))))))))).((((((..................)))))).....)).))))))......(((((..(....)..)).)))......)))))))))...))))..((....)).)))).......(((((...)))))......... (-86.27) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGUUUACGUGUGCAACACACUUUCCUUCUGCUGCAACAGCUUCUAUUUCAACCUUUUCUAAUAUAGGUAACGGUUUCCUUUUCCUGCUCAUUCUCUUAUAUUUGCUGCAAAGUUAGUUAUUUUUUUUGGUUUGCAUAGCAGCCUUGUGCUAAAACUGCUGAUACUGCUCUACUAUUCCAAACAACGUUACUUAUCAAUUAAAACGAAGUUGUAAAAACCUCUAAAAGCACUAUACAUAUUAUAUAUAACAAGCUUUUAUGGUUGUUUUCAAUAGUGUUUAAUGAUAAAAAGUUAAGAAUUGUUUUUGUUUUCUAUUAAAUAUUAUUAUCUUUGCUGCGUAAGACAGUAAACUCAGUAGAAUAUUUAAAAGAGAUUUAUGAAAAAGUUUUUCAUAGUGGCAGCU .........(((((...))))).........(((((...(((((.....(((............((((((((((.............((..((........))..)).(((..((((((..((((....((((.((...)))))).......))))..))))))..))).................))))))))))......(((((..((((....((((..(((((((.......................))))))).)))).....))))..)))))..)))....)))))...............(((((.(((((((((.((((.((((((((....).)))))))....))))))))))))).))))).((((((((.....))))))))..))))). (-75.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 337 292 216 167 pint:PI0002|5end_conserved_hypothetical_protein_2972..3202_POSITIVE 327 397 366 186 158 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 324 267 221 105 58 pint:PI2105|5end_hypothetical_protein_2059357..2059587_POSITIVE 324 300 257 116 76 pint:PI0198|5end_hypothetical_protein_190719..190949_POSITIVE 317 272 243 187 160 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 313 380 331 63 18 pint:PI0256|5end_conjugative_transposon_protein,_TraE_249044..249274_POSITIVE 306 276 234 145 108 pint:PI0937|5end_hypothetical_protein_869235..869465_POSITIVE 306 394 351 91 44 pint:PI0774|5end_phosphoserine_aminotransferase_(phosphoserine_transaminase)_709497..709727_POSITIVE 300 276 234 188 133 pint:PI1335|5end_Fe-S_oxidoreductase_1252818..1253048_POSITIVE 291 257 217 228 188 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 288 387 346 101 56 pint:PI1290|5end_ATP_synthase,_beta_subunit_1203059..1203289_POSITIVE 283 267 221 188 137 pint:PI2043|5end_hypothetical_protein_1996058..1996288_POSITIVE 273 395 355 106 68 pint:PI0946|5end_glutathione_peroxidase_877973..878203_POSITIVE 272 382 352 91 53 pint:PI1916|5end_conserved_hypothetical_protein_1860211..1860441_POSITIVE 272 398 351 121 62 pint:PI1565|5end_conserved_hypothetical_protein;_possible_surface_antigen_1485460..1485690_POSITIVE 272 399 360 120 84 pint:PI1359|5end_hypothetical_protein_1275473..1275703_POSITIVE 272 263 227 46 3 pint:PI0787|5end_glycosyltransferase_724136..724366_POSITIVE 272 277 231 136 87 pint:PI0454|5end_hypothetical_protein_426653..426883_POSITIVE 271 398 360 95 43 pint:PI1643|5end_conserved_hypothetical_protein_1560936..1561166_POSITIVE 270 399 364 110 70 pint:PI2049|5end_possible_transcriptional_regulator,_AraC_family_2002502..2002732_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 337 292 76 27 pint:PI0001|3end_possible_Ton-B_receptor_2912..3062_POSITIVE 324 267 221 58 11 pint:PI2104|3end_carboxyl-terminal_protease_2059390..2059540_POSITIVE 322 277 234 95 60 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 299 400 362 108 62 pint:PI2093|3end_hypothetical_protein_2049440..2049590_POSITIVE 299 400 362 74 28 pint:PI2092|3end_hypothetical_protein_2049406..2049556_POSITIVE 288 387 346 70 25 pint:PI1289|3end_ATP_synthase,_delta/epsilon_subunit_1203108..1203258_POSITIVE 284 398 353 114 67 pint:PI1803|3end_conserved_hypothetical_protein_1737791..1737941_POSITIVE 280 395 354 149 92 pint:PI0856|3end_hypothetical_protein_789927..790077_POSITIVE 274 276 235 55 11 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 272 399 360 83 47 pint:PI1358|3end_phospho-N-acetylmuramoyl-pentapeptide-transferase__1275516..1275666_POSITIVE 271 398 360 109 57 pint:PI1644|3end_hypothetical_protein_1561030..1561180_POSITIVE 270 399 364 94 54 pint:PI2048|3end_possible_two-component_system_sensor_histidine_kinase_2002566..2002716_POSITIVE 267 334 294 85 25 pint:PI0719|3end_conserved_hypothetical_protein_654010..654160_POSITIVE 262 224 181 149 106 pint:PI0888|3end_hypothetical_protein_818613..818763_POSITIVE 261 275 232 144 103 pint:PI0830|3end_conserved_hypothetical_protein_768206..768356_POSITIVE 259 399 364 89 51 pint:PI0227|3end_ABC_transporter,_ATP-binding/permease_protein_225632..225782_POSITIVE 256 237 193 151 109 pint:PI1809|3end_outer_membrane_protein_1748324..1748474_POSITIVE 255 397 351 115 63 pint:PI2008|3end__ABC_transporter,_ATP-binding_protein_1967961..1968111_POSITIVE 255 270 221 147 97 pint:PI0790|3end_hypothetical_protein_729206..729356_POSITIVE 255 276 245 137 104 pint:PI0782|3end_beta-lactamase_induction_signal_transducer,_AmpG_protein_721927..722077_POSITIVE