Origin IGS: gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa .........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 tttactgtacagtatcttttggatatcgatggtcctctccatgttacttgctatatgctttctaatttttccaagttctcaaatagagtgcaaatatagctaaaccttttgagatattcgacttttttataaaaaaaatactcaataaccattgatttgcacaccaaaaccaacgccaaagttgcacgtaaaaccacttgaaagcacacacaagcttcatttaaaacgtaatgaaaaatacttacaataagtcttttacacacttcttctacacctttactttgcgttaaatatattaaaaatacaagaataacgcaaactttgtggaggaaagaggtgaaatgtggggaattttacttaactttgaaccgaaatttcaattatataagaagtacac Mask Tandem Repeat Region ================================================ gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa Find is-nt database================================================ Query_seq: PI1899:PI1900|PI1899:PI1900:conserved hypothetical protein:conserved hypothetical protein:->->:1842842..1843238 397 gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1899:PI1900|PI1899:PI1900:conserved hypothetical protein:conserved hypothetical protein:->->:1842842..1843238 397 gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1899:PI1900|PI1899:PI1900:conserved hypothetical protein:conserved hypothetical protein:->->:1842842..1843238 397 gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 178 End: 333 ................................................................................................................................................................................. M K L V C A F K W F Y V Q L W R W F W C A N Q W L L S I F F I K K S N I S K G L A I F A L Y L R T W K N ................................................................ Protein_Len: 60 Strand: + Start: 87 End: 344 ...................................................................................... M L V F L I Y L T Q S K G V E E V C K R L I V S I F H Y V L N E A C V C F Q V V L R A T L A L V L V C K S M V I E Y F F ..................................................... Protein_Len: 32 Strand: - Start: 298 End: 393 ......................................................................................................................................................................................................................................................................................................... S Y K C E I Q S S P F I L F C I A L L M S L V M S I W F I S Y M .... Protein_Len: 32 Strand: - Start: 151 End: 246 ...................................................................................................................................................... Q L Y K E N R K L H L K H T S E L P K V H L K P T P K P T C I M ....................................................................................................................................................... Protein_Len: 53 Strand: - Start: 2 End: 160 . T S R I Y N F N R N L T L Y F E G C K V E K R W L T Q T I R T N K I Y K V C L L P T S S T H L L S I T L M ............................................................................................................................................................................................................................................. gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa 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: 79 End: 108 ..............................................................................TTTGCGTTATTCTTGTATTTTTAATATATT................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 44 HP_score: -2.4 Tail_Score: -3.2032 Start: 214 End: 227 Full_Region: AAGTGGTTTTACGTG CAAC TTTGGC GTTG GTTTTGGTGTGCAAA .....................................................................................................................................................................................................................CAACTTTGGCGTTG.......................................................................................................................................................................... Find igs database================================================ Query_seq: PI1899:PI1900|PI1899:PI1900:conserved hypothetical protein:conserved hypothetical protein:->->:1842842..1843238 397 gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 397 Len: 397 Subject: pint_PI1899_PI1900|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1842842,1843238]|397 HSP 1 e-value: 0.0 bit: 739.0 Len: 397 Query Start:1 Query End:397 Subject Strand: POSITIVE Subject Start: 1 Subject End: 397 gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtannnnnnnnataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa gtgtacttcttatataattgaaatttcggttcaaagttaagtaaaattccccacatttcacctctttcctccacaaagtttgcgttattcttgtatttttaatatatttaacgcaaagtaaaggtgtagaagaagtgtgtaaaagacttattgtaagtatttttcattacgttttaaatgaagcttgtgtgtgctttcaagtggttttacgtgcaactttggcgttggttttggtgtgcaaatcaatggttattgagtattttttttataaaaaagtcgaatatctcaaaaggtttagctatatttgcactctatttgagaacttggaaaaattagaaagcatatagcaagtaacatggagaggaccatcgatatccaaaagatactgtacagtaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUACUUCUUAUAUAAUUGAAAUUUCGGUUCAAAGUUAAGUAAAAUUCCCCACAUUUCACCUCUUUCCUCCACAAAGUUUGCGUUAUUCUUGUAUUUUUAAUAUAUUUAACGCAAAGUAAAGGUGUAGAAGAAGUGUGUAAAAGACUUAUUGUAAGUAUUUUUCAUUACGUUUUAAAUGAAGCUUGUGUGUGCUUUCAAGUGGUUUUACGUGCAACUUUGGCGUUGGUUUUGGUGUGCAAAUCAAUGGUUAUUGAGUAUUUUUUUUAUAAAAAAGUCGAAUAUCUCAAAAGGUUUAGCUAUAUUUGCACUCUAUUUGAGAACUUGGAAAAAUUAGAAAGCAUAUAGCAAGUAACAUGGAGAGGACCAUCGAUAUCCAAAAGAUACUGUACAGUAAA ...(((((.......((((((....)))))).......)))))........((((((((...(((..(((..((....(((((((((....(((((.....)))))..)))))))))))..)))...))).))))))))........(((((((((((((((((((((........))))).((((((((((((((((.(((..(((((.((.((((......))))....(((.((((((((..(((((((((((((((((..(((......)))..))))).)))))......))))))))))))))).))).......)).)))))..))).))))))))))).)))))....((((..(......)....)))).)))))))).)))))))). (-91.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACUGUACAGUAUCUUUUGGAUAUCGAUGGUCCUCUCCAUGUUACUUGCUAUAUGCUUUCUAAUUUUUCCAAGUUCUCAAAUAGAGUGCAAAUAUAGCUAAACCUUUUGAGAUAUUCGACUUUUUUAUAAAAAAAAUACUCAAUAACCAUUGAUUUGCACACCAAAACCAACGCCAAAGUUGCACGUAAAACCACUUGAAAGCACACACAAGCUUCAUUUAAAACGUAAUGAAAAAUACUUACAAUAAGUCUUUUACACACUUCUUCUACACCUUUACUUUGCGUUAAAUAUAUUAAAAAUACAAGAAUAACGCAAACUUUGUGGAGGAAAGAGGUGAAAUGUGGGGAAUUUUACUUAACUUUGAACCGAAAUUUCAAUUAUAUAAGAAGUACAC .....(((((.((...((((((..(((((((((..((((..........(((((((((.(((((...................))))).)))..))))))..........)))).....((..(((((.....)))))...))....))))))))).......))))))...))..((((((((...((((((((((.((((((...........((((((........))))))....(((((...)))))))))))..((((((((.....((((((((((((((((.....................)))))))))....))))))).))))))))....))))....)))))).)))))))).........................))))). (-74.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 257 211 210 175 pint:PI1781|5end_membrane-associated_zinc_metalloprotease_1713074..1713304_POSITIVE 334 230 182 83 31 pint:PI0049|5end_outer_membrane_receptor_protein_(iron_transport)_48605..48835_POSITIVE 332 255 216 73 33 pint:PI0052|5end_hypothetical_protein_52312..52542_POSITIVE 330 249 201 58 13 pint:PI2086|5end_signal_peptidase_I_2041835..2042065_POSITIVE 312 240 193 198 154 pint:PI0706|5end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_642226..642456_POSITIVE 310 239 192 56 16 pint:PI1688|5end_possible_GTPase_1602882..1603112_POSITIVE 307 167 122 155 117 pint:PI1982|5end_conserved_hypothetical_protein_1938439..1938669_POSITIVE 305 251 215 219 184 pint:PI1807|5end_hypothetical_protein_1742153..1742383_POSITIVE 303 238 191 100 53 pint:PI0141|5end_glutamine_amidotransferase_involved_in_pyridoxine_biosynthesis_132710..132940_POSITIVE 302 243 215 229 198 pint:PI1808|5end_LacI_family_transcriptional_regulator_1742167..1742397_POSITIVE 297 228 190 186 148 pint:PI1222|5end_hypothetical_protein_1142834..1143064_POSITIVE 296 258 211 152 100 pint:PI2106|5end_hypothetical_protein_2059221..2059451_POSITIVE 295 227 184 160 103 pint:PI1619|5end_two-component_system_response_regulator_1543210..1543440_POSITIVE 293 237 191 78 41 pint:PI0618|5end_acyl-CoA_dehydrogenase_family_protein_567409..567639_POSITIVE 289 240 192 214 162 pint:PI0827|5end_hypothetical_protein_763991..764221_POSITIVE 288 228 183 54 16 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 284 216 183 148 109 pint:PI2035|5end_Holliday_junction_DNA_helicase_ruvB_1988212..1988442_POSITIVE 283 259 216 93 46 pint:PI0540|5end_conserved_hypothetical_protein_492955..493185_POSITIVE 281 240 198 106 62 pint:PI1663|5end_hypothetical_protein_1577127..1577357_POSITIVE 280 240 192 71 24 pint:PI1679|5end_hypothetical_protein_1594744..1594974_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 248 201 147 93 pint:PI0981|3end_outer_membrane_protein,_TonB_dependent_receptor_909390..909540_POSITIVE 319 248 201 148 110 pint:PI1780|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1713097..1713247_POSITIVE 310 240 192 149 97 pint:PI0638|3end_hypothetical_protein_582402..582552_POSITIVE 310 240 192 144 92 pint:PI0637|3end_hypothetical_protein_582397..582547_POSITIVE 307 166 122 51 14 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 306 239 192 81 28 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 299 239 195 100 39 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 297 228 190 127 89 pint:PI1221|3end_penicillin-binding_protein_1A_1142855..1143005_POSITIVE 293 237 191 55 18 pint:PI0617|3end_electron_transfer_flavoprotein,_alpha_subunit_567466..567616_POSITIVE 291 255 216 93 47 pint:PI1547|3end_hypothetical_protein_1466226..1466376_POSITIVE 288 228 183 63 25 pint:PI0300|3end_transposase_285761..285911_POSITIVE 281 230 183 151 107 pint:PI1773|3end_alpha-amylase_(neopullulanase)_1706107..1706257_POSITIVE 281 240 198 140 96 pint:PI1662|3end_hypothetical_protein_1577241..1577391_POSITIVE 280 240 192 100 48 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 279 240 191 117 75 pint:PI1206|3end_ATP-dependent_DNA_helicase,_UvrD/PcrA/Rep_family_1127132..1127282_POSITIVE 278 248 201 69 19 pint:PI2148|3end_ribonuclease_III_2095541..2095691_POSITIVE 277 240 198 140 96 pint:PI0369|3end_hypothetical_protein_340409..340559_POSITIVE 276 240 199 123 75 pint:PI0551|3end_hypothetical_protein_502683..502833_POSITIVE 274 248 203 133 78 pint:PI1798|3end__elongation_factor_Ts_1732824..1732974_POSITIVE 274 237 193 77 25 pint:PI1226|3end_hypothetical_protein_1148263..1148413_POSITIVE