Origin IGS: tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta .........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 taacaaaagcaagcacatcttgaacttctcggttcttgatgtgcttgctttttttataatagcattttaaagtaattcaatagctattgatactttatgctgaaaagcacaccgtttcgcttttccaagtagaaagaactctttagctccctacaccgtaagccctccattcctcatttcagaaacggaaaacgaactataaagctgtaaatatttttcacaacaataagtattacataatctcctcgttatcaatgca Mask Tandem Repeat Region ================================================ tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta Find is-nt database================================================ Query_seq: PI1041:PI1043|PI1041:PI1043:hypothetical protein:conserved hypothetical protein:->->:960736..960994 259 tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1041:PI1043|PI1041:PI1043:hypothetical protein:conserved hypothetical protein:->->:960736..960994 259 tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1041:PI1043|PI1041:PI1043:hypothetical protein:conserved hypothetical protein:->->:960736..960994 259 tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 5 End: 106 .... M I T R R L C N T Y C C E K Y L Q L Y S S F S V S E M R N G G L T V ......................................................................................................................................................... tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta 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================================================ tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1041:PI1043|PI1041:PI1043:hypothetical protein:conserved hypothetical protein:->->:960736..960994 259 tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta Intra-Species Hit: Count: 1 Min: 1 Max: 259 Len: 259 Subject: pint_PI1041_PI1043|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[960736,960994]|259 HSP 1 e-value: 1.0E-132 bit: 472.0 Len: 259 Query Start:1 Query End:259 Subject Strand: POSITIVE Subject Start: 1 Subject End: 259 tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattatnnnnnnngcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta tgcattgataacgaggagattatgtaatacttattgttgtgaaaaatatttacagctttatagttcgttttccgtttctgaaatgaggaatggagggcttacggtgtagggagctaaagagttctttctacttggaaaagcgaaacggtgtgcttttcagcataaagtatcaatagctattgaattactttaaaatgctattataaaaaaagcaagcacatcaagaaccgagaagttcaagatgtgcttgcttttgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAUUGAUAACGAGGAGAUUAUGUAAUACUUAUUGUUGUGAAAAAUAUUUACAGCUUUAUAGUUCGUUUUCCGUUUCUGAAAUGAGGAAUGGAGGGCUUACGGUGUAGGGAGCUAAAGAGUUCUUUCUACUUGGAAAAGCGAAACGGUGUGCUUUUCAGCAUAAAGUAUCAAUAGCUAUUGAAUUACUUUAAAAUGCUAUUAUAAAAAAAGCAAGCACAUCAAGAACCGAGAAGUUCAAGAUGUGCUUGCUUUUGUUA .(((((.....((((.(((.......((((.((..((((((((.....))))))))..))..((..(((((((((((((......)))))))))))))..)).))))..((((((....)))))).))).))))((((((((........))))))))....((((((((((((....)))))..))))))).))))).........(((((((((((((((..((((......))))..))))))))))))))).... (-80.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAAAGCAAGCACAUCUUGAACUUCUCGGUUCUUGAUGUGCUUGCUUUUUUUAUAAUAGCAUUUUAAAGUAAUUCAAUAGCUAUUGAUACUUUAUGCUGAAAAGCACACCGUUUCGCUUUUCCAAGUAGAAAGAACUCUUUAGCUCCCUACACCGUAAGCCCUCCAUUCCUCAUUUCAGAAACGGAAAACGAACUAUAAAGCUGUAAAUAUUUUUCACAACAAUAAGUAUUACAUAAUCUCCUCGUUAUCAAUGCA (((.(((((((((((((((..(((((....)))))..))))))))))))))).))).....(((((.(((((((..(((((....)))))))))))).(((....)))...(((((((..(((((......))))).........(((..(......)..)))..................)))))))..(((((..........(((((.(((((...........))))))))))........)))))...))))). (-63.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 64 21 167 124 pint:PI1346|5end_hypothetical_protein_1260814..1261044_POSITIVE 414 77 37 207 167 pint:PI0851|5end_hypothetical_protein_784310..784540_POSITIVE 389 110 61 125 82 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 356 128 82 75 20 pint:PI0609|5end_conserved_hypothetical_protein_556519..556749_POSITIVE 355 50 1 114 60 pint:PI0099|5end_hypothetical_protein_95530..95760_POSITIVE 343 50 2 136 88 pint:PI1195|5end_hypothetical_protein_1113171..1113401_POSITIVE 333 60 14 163 113 pint:PI1694|5end_hypothetical_protein_1609717..1609947_POSITIVE 329 113 71 127 91 pint:PI1664|5end_conserved_hypothetical_protein_1577285..1577515_POSITIVE 329 113 71 127 91 pint:PI0370|5end_conserved_hypothetical_protein_340453..340683_POSITIVE 325 135 91 62 16 pint:PI0034|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_37151..37381_POSITIVE 324 80 35 86 46 pint:PI0689|5end_hypothetical_protein_625624..625854_POSITIVE 323 89 41 74 26 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 317 114 72 187 134 pint:PI0432|5end_hypothetical_protein_404781..405011_POSITIVE 317 114 72 130 77 pint:PI0433|5end_hypothetical_protein_404724..404954_POSITIVE 312 130 86 165 110 pint:PI0776|5end_predicted_TPR-repeat-containing_protein_712077..712307_POSITIVE 310 108 65 156 116 pint:PI0737|5end_hypothetical_protein_671182..671412_POSITIVE 308 114 72 62 21 pint:PI1736|5end_topoisomerase_IV,_subunit_A_1654254..1654484_POSITIVE 307 249 208 91 55 pint:PI1522|5end_thioredoxin_M_1441646..1441876_POSITIVE 304 116 75 193 155 pint:PI1879|5end_uracil_phosphoribosyltransferase_1820671..1820901_POSITIVE 303 161 121 158 110 pint:PI1726|5end_ATP-dependent_DNA_helicase_1643402..1643632_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 110 61 65 22 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 356 128 82 56 1 pint:PI0608|3end_isochorismate_synthase_556580..556730_POSITIVE 329 113 71 109 73 pint:PI1663|3end_hypothetical_protein_1577347..1577497_POSITIVE 325 50 1 88 34 pint:PI1813|3end_hypothetical_protein_1753086..1753236_POSITIVE 324 80 35 132 92 pint:PI0688|3end_hypothetical_protein_625750..625900_POSITIVE 323 89 41 141 93 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 315 58 13 47 1 pint:PI1424|3end_probable_peptidase_family_M48_1344044..1344194_POSITIVE 308 114 72 51 10 pint:PI1735|3end_conserved_hypothetical_protein_1654323..1654473_POSITIVE 306 70 35 60 18 pint:PI0770|3end_hypothetical_protein_706354..706504_POSITIVE 302 130 82 122 64 pint:PI2096|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2050884..2051034_POSITIVE 300 177 133 149 99 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 298 116 86 151 120 pint:PI0775|3end_ATP-independent_RNA_helicase_712167..712317_POSITIVE 297 129 85 144 85 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 296 148 102 67 17 pint:PI0411|3end_conserved_hypothetial_protein;_possible_hydrolase_379828..379978_POSITIVE 295 155 116 76 37 pint:PI1688|3end_possible_GTPase_1603903..1604053_POSITIVE 290 110 63 71 30 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 289 50 1 57 3 pint:PI0051|3end_hypothetical_protein_53388..53538_POSITIVE 287 57 11 145 97 pint:PI0996|3end_hypothetical_protein_920660..920810_POSITIVE 286 245 214 148 118 pint:PI2006|3end_potassium_uptake_system_protein_1965846..1965996_POSITIVE 286 110 61 56 10 pint:PI1982|3end_conserved_hypothetical_protein_1939208..1939358_POSITIVE