Origin IGS: tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttatactatgaatattcgtgatttcttttacttgcagaagtccgacagaaaggtaattgctttcttgctatgccttgccgttgccgtattgggagcgatattcctgttaggcaacaagaaccctcgcaca Mask Tandem Repeat Region ================================================ tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag Find is-nt database================================================ Query_seq: PI0056:PI0057|PI0056:PI0057:conserved hypothetical protein; possible DNA uptake protein:conserved hypothetical protein:->->:55968..56098 131 tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0056:PI0057|PI0056:PI0057:conserved hypothetical protein; possible DNA uptake protein:conserved hypothetical protein:->->:55968..56098 131 tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0056:PI0057|PI0056:PI0057:conserved hypothetical protein; possible DNA uptake protein:conserved hypothetical protein:->->:55968..56098 131 tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 2 End: 100 . M R G F L L P N R N I A P N T A T A R H S K K A I T F L S D F C K ............................... Protein_Len: 31 Strand: + Start: 30 End: 122 ............................. M S L P I R Q R Q G I A R K Q L P F C R T S A S K R N H E Y S ......... Protein_Len: 41 Strand: - Start: 1 End: 123 T R P N K N G L L F I A G L V A V A L C L L F A I V K R D S K Q L Y F F D R I N M ........ tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag 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================================================ tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.3 Tail_Score: -3.29739 Start: 67 End: 83 Full_Region: tgcagaagtccgaca gaaag gtaattg ctttc ttgctatgccttgcc ..................................................................gaaaggtaattgctttc................................................ Find igs database================================================ Query_seq: PI0056:PI0057|PI0056:PI0057:conserved hypothetical protein; possible DNA uptake protein:conserved hypothetical protein:->->:55968..56098 131 tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: pint_PI0056_PI0057|conserved hypothetical protein; possible DNA uptake protein:conserved hypothetical protein|POSITIVE:POSITIVE|[55968,56098]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag tgtgcgagggttcttgttgcctaacaggaatatcgctcccaatacggcaacggcaaggcatagcaagaaagcaattacctttctgtcggacttctgcaagtaaaagaaatcacgaatattcatagtataag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUGCGAGGGUUCUUGUUGCCUAACAGGAAUAUCGCUCCCAAUACGGCAACGGCAAGGCAUAGCAAGAAAGCAAUUACCUUUCUGUCGGACUUCUGCAAGUAAAAGAAAUCACGAAUAUUCAUAGUAUAAG (((((..(..((((((((((((....(((.......))).....((....))...)))))..)))))))..).............(((((.((((.........)))).)).))).........))))).. (-29.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUACUAUGAAUAUUCGUGAUUUCUUUUACUUGCAGAAGUCCGACAGAAAGGUAAUUGCUUUCUUGCUAUGCCUUGCCGUUGCCGUAUUGGGAGCGAUAUUCCUGUUAGGCAACAAGAACCCUCGCACA ................(((.(((((((.........))))))))))....((((((...((......))..))))))...((((((.....((((......)))).....))))))............... (-31.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 47 1 110 60 pint:PI1837|5end_aspartate_ammonia-lyase_1778953..1779183_POSITIVE 389 59 14 66 6 pint:PI1749|5end_conserved_hypothetical_protein_1671039..1671269_POSITIVE 371 48 2 106 49 pint:PI1763|5end_two-component_system_sensor_histidine_kinase/response_regulator_1685877..1686107_POSITIVE 343 60 14 163 116 pint:PI0737|5end_hypothetical_protein_671182..671412_POSITIVE 338 49 1 81 30 pint:PI0189|5end_integrase_179623..179853_POSITIVE 335 80 34 201 144 pint:PI0478|5end_50S_ribosomal_protein_L30_440923..441153_POSITIVE 334 68 23 61 4 pint:PI0595|5end_conserved_hypothetical_protein_545571..545801_POSITIVE 333 50 1 199 147 pint:PI0951|5end_hypothetical_protein_884526..884756_POSITIVE 332 59 15 70 19 pint:PI0680|5end_hypothetical_protein_616958..617188_POSITIVE 322 90 45 90 36 pint:PI1887|5end_cell_division_protein_1829115..1829345_POSITIVE 321 48 3 70 16 pint:PI1829|5end_hypothetical_protein_1769255..1769485_POSITIVE 316 59 14 54 19 pint:PI1707|5end_GTP-binding_protein_1623795..1624025_POSITIVE 309 69 26 90 37 pint:PI1565|5end_conserved_hypothetical_protein;_possible_surface_antigen_1485460..1485690_POSITIVE 308 58 12 177 139 pint:PI0222|5end_conserved_hypothetical_protein_217808..218038_POSITIVE 305 48 3 142 101 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 301 48 3 70 16 pint:PI1076|5end_hypothetical_protein_998893..999123_POSITIVE 299 97 52 48 1 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 294 59 15 54 1 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 293 48 1 128 58 pint:PI1735|5end_conserved_hypothetical_protein_1653428..1653658_POSITIVE 292 69 24 86 37 pint:PI0845|5end_peptidyl-dipeptidase_778272..778502_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 48 1 127 72 pint:PI0721|3end_hypothetical_protein_654982..655132_POSITIVE 314 90 43 53 5 pint:PI1886|3end_cell_division_protein_1829158..1829308_POSITIVE 308 58 12 85 47 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 307 59 15 56 19 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 298 59 15 55 6 pint:PI0245|3end_possible_mobilization_protein_244258..244408_POSITIVE 295 59 11 116 61 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 294 50 8 46 5 pint:PI1006|3end_conserved_hypothetical_protein_927049..927199_POSITIVE 294 59 15 54 1 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 292 69 24 50 1 pint:PI0844|3end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_778316..778466_POSITIVE 292 50 4 58 5 pint:PI0419|3end_conserved_hypothetical_protein_387461..387611_POSITIVE 290 67 23 107 61 pint:PI1736|3end_topoisomerase_IV,_subunit_A_1657090..1657240_POSITIVE 289 59 14 135 73 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 288 70 24 53 17 pint:PI2151|3end_conserved_hypothetical_protein_2098252..2098402_POSITIVE 288 80 34 134 67 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE 287 46 13 135 103 pint:PI0396|3end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_362396..362546_POSITIVE 285 54 13 145 103 pint:PI0241|3end_possible_tetracycline_resistance_element_/mobilization_regulatory_protein_240036..240186_POSITIVE 283 48 3 112 58 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 283 97 51 47 2 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 282 48 3 120 80 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 281 50 1 139 92 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE