Origin IGS: taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatggaatatggtgcggttttagttgcaatatgataaaataatatgagtgggattgcctgtttaagggcaatcccacttgcgtttttttagaagttaatggtgtttttgcattagaaaattatgaaccatgatta Mask Tandem Repeat Region ================================================ taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca Find is-nt database================================================ Query_seq: PI1756:PI1758|PI1756:PI1758:conserved hypothetical protein:hypothetical protein:->->:1683211..1683346 136 taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1756:PI1758|PI1756:PI1758:conserved hypothetical protein:hypothetical protein:->->:1683211..1683346 136 taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1756:PI1758|PI1756:PI1758:conserved hypothetical protein:hypothetical protein:->->:1683211..1683346 136 taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca Predict ORF larger than 30AA ================================================ taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca 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================================================ taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.9 Tail_Score: -5.43866 Start: 54 End: 93 Full_Region: aatatgataaaataa tatgagtgggattgcct gtttaa gggcaatcccacttgcg tttttttagaagtta .....................................................tatgagtgggattgcctgtttaagggcaatcccacttgcg........................................... TransTerm Strand: - Conf: 81 HP_score: -9.2 Tail_Score: -3.85235 Start: 55 End: 92 Full_Region: atatgataaaataat atgagtgggattgcct gtttaa gggcaatcccacttgc gtttttttagaagtt ......................................................atgagtgggattgcctgtttaagggcaatcccacttgc............................................ TransTerm Strand: - Conf: 100 HP_score: -14.4 Tail_Score: -3.58247 Start: 59 End: 88 Full_Region: gataaaataatatga gtgggattgcct gtttaa gggcaatcccac ttgcgtttttttaga ..........................................................gtgggattgcctgtttaagggcaatcccac................................................ Find igs database================================================ Query_seq: PI1756:PI1758|PI1756:PI1758:conserved hypothetical protein:hypothetical protein:->->:1683211..1683346 136 taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: pint_PI1756_PI1758|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1683211,1683346]|136 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 taatcatggttcataattttctaatgcaaaaacaccattaacttctnnnnnnncgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca taatcatggttcataattttctaatgcaaaaacaccattaacttctaaaaaaacgcaagtgggattgcccttaaacaggcaatcccactcatattattttatcatattgcaactaaaaccgcaccatattccatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAUGGUUCAUAAUUUUCUAAUGCAAAAACACCAUUAACUUCUAAAAAAACGCAAGUGGGAUUGCCCUUAAACAGGCAAUCCCACUCAUAUUAUUUUAUCAUAUUGCAACUAAAACCGCACCAUAUUCCAUCA .....(((((.(.........(((((.........)))))..............(((((((((((((((........))))))))))))..................)))..........).)))))......... (-28.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGGAAUAUGGUGCGGUUUUAGUUGCAAUAUGAUAAAAUAAUAUGAGUGGGAUUGCCUGUUUAAGGGCAAUCCCACUUGCGUUUUUUUAGAAGUUAAUGGUGUUUUUGCAUUAGAAAAUUAUGAACCAUGAUUA ..((((..((((((....(((((((.((((.((..(((((.(((..((((((((((((((......))))))))))))))..))).)))))...))...........))))))))))).))))))..))))..... (-41.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 88 57 106 75 pint:PI1005|5end_hypothetical_protein_926201..926431_POSITIVE 352 86 43 146 106 pint:PI0820|5end_hypothetical_protein_759694..759924_POSITIVE 306 79 33 134 81 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 305 97 54 178 119 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 299 80 32 57 6 pint:PI0604|5end_O-succinylbenzoic_acid--CoA_ligase_550825..551055_POSITIVE 278 84 59 222 197 pint:PI0294|5end_conserved_hypothetical_protein_276223..276453_POSITIVE 263 90 54 194 154 pint:PI0506|5end_conserved_hypothetical_protein_465501..465731_POSITIVE 258 70 24 62 13 pint:PI2066|5end_hypothetical_protein_2027179..2027409_POSITIVE 251 88 53 115 73 pint:PI1723|5end_conserved_hypothetical_protein_1641649..1641879_POSITIVE 251 84 52 39 9 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 251 98 56 126 83 pint:PI0168|5end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_161181..161411_POSITIVE 249 79 54 223 193 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 248 90 68 102 79 pint:PI0500|5end_mobilizable_transposon,_tnpC_protein_460674..460904_POSITIVE 248 86 51 221 185 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 243 100 52 223 169 pint:PI0608|5end_isochorismate_synthase_555487..555717_POSITIVE 240 88 59 149 120 pint:PI1259|5end_ISPg4-related_transposase_(IS5_family)_1180741..1180971_POSITIVE 234 88 42 54 13 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 231 81 50 222 190 pint:PI1868|5end_hypothetical_protein_1814638..1814868_POSITIVE 231 96 55 81 36 pint:PI0591|5end_adenylosuccinate_lyase_538595..538825_POSITIVE 228 69 32 46 3 pint:PI1368|5end_enolase_(phosphopyruvate_hydratase)_1288123..1288353_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 88 57 42 11 pint:PI1004|3end_conserved_hypothetical_protein_926217..926367_POSITIVE 385 89 58 33 2 pint:PI1756|3end_conserved_hypothetical_protein_1683150..1683300_POSITIVE 320 86 59 31 4 pint:PI0818|3end_alpha-amylase_759659..759809_POSITIVE 258 70 24 56 7 pint:PI2065|3end_hypothetical_protein_2027253..2027403_POSITIVE 255 123 85 82 44 pint:PI0242|3end_hypothetical_protein_240227..240377_POSITIVE 251 98 56 123 80 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 248 86 50 38 2 pint:PI1748|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase/possible_(p)ppgpp_synthetase_II_1670922..1671072_POSITIVE 232 86 43 142 97 pint:PI1629|3end_hypothetical_protein_1551966..1552116_POSITIVE 227 90 54 52 21 pint:PI0055|3end_hypothetical_protein_55044..55194_POSITIVE 227 90 54 132 101 pint:PI0053|3end_hypothetical_protein_55124..55274_POSITIVE 224 80 33 54 7 pint:PI1605|3end_conserved_hypothetical_protein_1535178..1535328_POSITIVE 220 98 53 82 40 pint:PI1647|3end_hypothetical_protein_1562531..1562681_POSITIVE 220 82 41 150 105 pint:PI1335|3end_Fe-S_oxidoreductase_1253569..1253719_POSITIVE 220 98 53 82 40 pint:PI0353|3end_hypothetical_protein_325337..325487_POSITIVE 216 94 53 129 79 pint:PI0726|3end_hypothetical_protein_659253..659403_POSITIVE 212 87 54 148 108 pint:PI1535|3end_response_regulator_1455501..1455651_POSITIVE 212 112 74 106 67 pint:PI1450|3end_hypothetical_protein_1372891..1373041_POSITIVE 209 80 33 116 75 pint:PI0225|3end_conserved_hypothetical_protein_222759..222909_POSITIVE 208 80 34 57 3 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 207 96 55 83 33 pint:PI0308|3end_conserved_hypothetical_protein_291602..291752_POSITIVE