Origin IGS: tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattcgttcaagttttccttggaggatggatatataacccatcctaattcgcatagcctggtggtagtaggacaacacatacacagactgggtacgcgta Mask Tandem Repeat Region ================================================ tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta Find is-nt database================================================ Query_seq: PI1973:PI1974|PI1973:PI1974:conserved hypothetical protein:hypothetical protein:->->:1931232..1931332 101 tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1973:PI1974|PI1973:PI1974:conserved hypothetical protein:hypothetical protein:->->:1931232..1931332 101 tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1973:PI1974|PI1973:PI1974:conserved hypothetical protein:hypothetical protein:->->:1931232..1931332 101 tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta Predict ORF larger than 30AA ================================================ tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta 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================================================ tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1973:PI1974|PI1973:PI1974:conserved hypothetical protein:hypothetical protein:->->:1931232..1931332 101 tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: pint_PI1973_PI1974|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1931232,1931332]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta tacgcgtacccagtctgtgtatgtgttgtcctactaccaccaggctatgcgaattaggatgggttatatatccatcctccaaggaaaacttgaacgaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACGCGUACCCAGUCUGUGUAUGUGUUGUCCUACUACCACCAGGCUAUGCGAAUUAGGAUGGGUUAUAUAUCCAUCCUCCAAGGAAAACUUGAACGAAUUA ..(((((....((((((((...(((......)))...)).)))))))))))....(((((((((.....))))))))).((((.....))))......... (-28.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCGUUCAAGUUUUCCUUGGAGGAUGGAUAUAUAACCCAUCCUAAUUCGCAUAGCCUGGUGGUAGUAGGACAACACAUACACAGACUGGGUACGCGUA .......((((((.....))))))((((((.........)))))).....(((...(((..((.((.((((.......).)))))..))..)))..))).. (-24.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 49 3 86 33 pint:PI1783|5end_possible_4-diphosphocytidyl-2c-methyl-D-erythritol_synthase_1715362..1715592_POSITIVE 306 45 3 48 1 pint:PI1731|5end_formate--tetrahydrofolate_ligase_1650122..1650352_POSITIVE 299 80 36 161 120 pint:PI2076|5end_hypothetical_protein_2035403..2035633_POSITIVE 299 56 11 164 117 pint:PI1626|5end_hypothetical_protein_1550194..1550424_POSITIVE 298 80 32 89 36 pint:PI1001|5end_hypothetical_protein_923510..923740_POSITIVE 296 48 4 194 144 pint:PI0601|5end_hypothetical_protein_548758..548988_POSITIVE 287 79 42 178 140 pint:PI0409|5end_3-deoxy-D-manno-octulosonic-acid_transferase_(kdotransferase)_374648..374878_POSITIVE 284 68 21 81 27 pint:PI0767|5end_possible_TonB-dependent_receptor_701915..702145_POSITIVE 283 58 11 95 47 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 277 61 23 41 3 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 277 49 4 173 121 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 273 45 4 86 31 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 270 89 43 83 28 pint:PI0272|5end_conserved_hypothetical_protein_262621..262851_POSITIVE 269 85 42 188 139 pint:PI0275|5end_hypothetical_protein_263138..263368_POSITIVE 267 64 22 113 69 pint:PI1494|5end_conserved_hypothetical_protein_1413046..1413276_POSITIVE 267 50 3 159 111 pint:PI0985|5end_aspartyl-tRNA_synthetase_910174..910404_POSITIVE 267 49 4 230 187 pint:PI0464|5end_30S_ribosomal_protein_S19_435008..435238_POSITIVE 264 49 2 71 9 pint:PI1826|5end_ATP-dependent_DNA_helicase_1765650..1765880_POSITIVE 264 65 21 56 1 pint:PI0479|5end_50S_ribosomal_protein_L15_441125..441355_POSITIVE 263 57 12 170 121 pint:PI0726|5end_hypothetical_protein_659042..659272_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 42 3 81 30 pint:PI0962|3end_phosphoglycerate_mutase_892702..892852_POSITIVE 327 50 3 62 5 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 317 58 13 92 33 pint:PI0005|3end_hypothetical_protein_7450..7600_POSITIVE 302 50 2 49 11 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 286 50 2 111 63 pint:PI0718|3end_hypothetical_protein_654212..654362_POSITIVE 284 68 21 62 8 pint:PI0766|3end_conserved_hypothetical_protein_701976..702126_POSITIVE 283 58 11 86 38 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 282 50 5 121 70 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 281 50 3 148 88 pint:PI0115|3end_hypothetical_protein_108669..108819_POSITIVE 277 49 4 150 98 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 276 44 4 146 103 pint:PI0600|3end_bifunctional_purine_biosynthesis_protein,_5-aminoimidazole-4-carboxamide_ribonucleotide(AICAR)_transformylase/IMP_cyclohydrolase_548797..548947_POSITIVE 271 49 1 108 60 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 267 50 3 49 1 pint:PI0984|3end_hypothetical_protein_910144..910294_POSITIVE 262 50 4 108 55 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 262 46 9 57 18 pint:PI0052|3end_hypothetical_protein_52715..52865_POSITIVE 257 55 12 89 38 pint:PI0278|3end_hypothetical_protein_265625..265775_POSITIVE 255 49 2 134 63 pint:PI0125|3end_undecaprenyl_pyrophosphate_synthase_117890..118040_POSITIVE 254 50 3 93 43 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 253 58 14 149 98 pint:PI1849|3end_conserved_hypothetical_protein;_possible_acyltransferase_family_protein_1796039..1796189_POSITIVE 253 63 37 61 24 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE