Origin IGS: atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta .........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 taggaaaacggaatgttgtttatgctcatactaaatttgaaggaactagagatattcccgtcaaagcacgattctattatagaagtttgaatggaaaggaatatcttaccgattttgcaccgcttcagatagaacaagatggcacgacaaaggttgagctttcactgacggacactcaggcagaagaaataaagaatatgcagacagaaaagacgttgatctat Mask Tandem Repeat Region ================================================ atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta Find is-nt database================================================ Query_seq: PI1966:PI1967|PI1966:PI1967:conserved hypothetical protein:hypothetical protein:->->:1924152..1924375 224 atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1966:PI1967|PI1966:PI1967:conserved hypothetical protein:hypothetical protein:->->:1924152..1924375 224 atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1966:PI1967|PI1966:PI1967:conserved hypothetical protein:hypothetical protein:->->:1924152..1924375 224 atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 18 End: 116 ................. M S A Y S L F L L P E C P S V K A Q P L S C H L V L S E A V Q N R ............................................................................................................ Protein_Len: 46 Strand: + Start: 85 End: 222 .................................................................................... M L F Y L K R C K I G K I F L S I Q T S I I E S C F D G N I S S S F K F S M S I N N I P F S .. Protein_Len: 57 Strand: - Start: 1 End: 171 Y I L T K E T Q M N K I E E A Q T D T L S L E V K T T G D Q E I Q L P A F D T L Y E K G N L S R Y Y F R A K V P M ..................................................... atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta 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================================================ atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1966:PI1967|PI1966:PI1967:conserved hypothetical protein:hypothetical protein:->->:1924152..1924375 224 atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta Intra-Species Hit: Count: 1 Min: 1 Max: 224 Len: 224 Subject: pint_PI1966_PI1967|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1924152,1924375]|224 HSP 1 e-value: 1.0E-124 bit: 444.0 Len: 224 Query Start:1 Query End:224 Subject Strand: POSITIVE Subject Start: 1 Subject End: 224 atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta atagatcaacgtcttttctgtctgcatattctttatttcttctgcctgagtgtccgtcagtgaaagctcaacctttgtcgtgccatcttgttctatctgaagcggtgcaaaatcggtaagatattcctttccattcaaacttctataatagaatcgtgctttgacgggaatatctctagttccttcaaatttagtatgagcataaacaacattccgttttccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGAUCAACGUCUUUUCUGUCUGCAUAUUCUUUAUUUCUUCUGCCUGAGUGUCCGUCAGUGAAAGCUCAACCUUUGUCGUGCCAUCUUGUUCUAUCUGAAGCGGUGCAAAAUCGGUAAGAUAUUCCUUUCCAUUCAAACUUCUAUAAUAGAAUCGUGCUUUGACGGGAAUAUCUCUAGUUCCUUCAAAUUUAGUAUGAGCAUAAACAACAUUCCGUUUUCCUA .(((...((((.((((((((.(.(.((((((................))))))).).))).)))))........((((.(((((((.(((....((.(((((((((.....))))...((((((((((.((.(..((...(((((...)))))...))..).)).)))))))))).......))))).)).))).))).))))..)))).....))))...))) (-38.99) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAAAACGGAAUGUUGUUUAUGCUCAUACUAAAUUUGAAGGAACUAGAGAUAUUCCCGUCAAAGCACGAUUCUAUUAUAGAAGUUUGAAUGGAAAGGAAUAUCUUACCGAUUUUGCACCGCUUCAGAUAGAACAAGAUGGCACGACAAAGGUUGAGCUUUCACUGACGGACACUCAGGCAGAAGAAAUAAAGAAUAUGCAGACAGAAAAGACGUUGAUCUAU ((((..((((.....(((((..(((.......................((((((((((..((....((...(((((...)))))...))....))..))))))))))....(((((......((((...........((.(((.((((....)))).))).)).((((.(....)))))...))))......)))))..))))))))......))))..)))). (-47.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 88 41 194 145 pint:PI2109|5end_surface_antigen_BspA_2060553..2060783_POSITIVE 369 78 31 131 76 pint:PI0819|5end_hypothetical_protein_759414..759644_POSITIVE 357 90 42 76 28 pint:PI0146|5end_transcription_elongation_factor_140338..140568_POSITIVE 339 109 66 163 120 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 334 84 43 73 22 pint:PI1568|5end_OmpA_family_protein_1489584..1489814_POSITIVE 327 117 73 71 25 pint:PI0463|5end_50S_ribosomal_protein_L2_434158..434388_POSITIVE 324 119 71 65 12 pint:PI1795|5end_conserved_hypothetical_protein_1726864..1727094_POSITIVE 322 90 46 55 7 pint:PI0467|5end_50S_ribosomal_protein_L16_436471..436701_POSITIVE 319 115 75 87 42 pint:PI1745|5end_conserved_hypothetical_protein_1666615..1666845_POSITIVE 318 100 51 221 165 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 314 108 61 117 64 pint:PI0613|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_562167..562397_POSITIVE 310 78 39 49 1 pint:PI0580|5end_Holliday_junction_DNA_helicase_524178..524408_POSITIVE 308 105 61 146 92 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 306 110 65 130 75 pint:PI0129|5end_hypothetical_protein_121709..121939_POSITIVE 305 88 42 154 119 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 304 107 65 55 11 pint:PI0485|5end_30S_ribosomal_protein_S4_444450..444680_POSITIVE 301 67 21 151 105 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 300 120 71 204 142 pint:PI1767|5end_fructokinase,_pfkB_family_1694285..1694515_POSITIVE 300 86 42 131 86 pint:PI0118|5end_hypothetical_protein_111321..111551_POSITIVE 298 88 43 101 55 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 117 73 60 14 pint:PI0462|3end_50S_ribosomal_protein_L23_434227..434377_POSITIVE 321 73 36 151 104 pint:PI2085|3end_conserved_hypothetical_protein_2041803..2041953_POSITIVE 314 108 61 72 19 pint:PI0612|3end_lysyl-tRNA_synthetase_562202..562352_POSITIVE 304 105 65 141 90 pint:PI0639|3end_small_heat_shock_protein_583165..583315_POSITIVE 303 90 43 144 95 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 302 53 20 55 23 pint:PI1654|3end_hypothetical_protein_1567958..1568108_POSITIVE 301 118 72 151 99 pint:PI0353|3end_hypothetical_protein_325337..325487_POSITIVE 301 67 21 97 51 pint:PI0265|3end_conjugative_transposon_protein,_TraO_257957..258107_POSITIVE 300 85 41 147 104 pint:PI1229|3end_conserved_hypothetical_protein_1151669..1151819_POSITIVE 294 108 73 100 58 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 292 62 24 148 103 pint:PI0309|3end_hypothetical_protein_291729..291879_POSITIVE 292 110 64 96 53 pint:PI0118|3end_hypothetical_protein_111640..111790_POSITIVE 290 84 46 43 2 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 289 58 12 151 96 pint:PI0414|3end_hypothetical_protein_385210..385360_POSITIVE 286 87 47 133 88 pint:PI2032|3end_RNA_polymerase_sigma_factor,_ECF_subfamily_1987121..1987271_POSITIVE 284 125 82 49 9 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 283 109 61 118 58 pint:PI0052|3end_hypothetical_protein_52715..52865_POSITIVE 283 109 61 74 14 pint:PI0050|3end_conserved_hypothetical_protein_52671..52821_POSITIVE 282 88 44 51 5 pint:PI1175|3end_conserved_hypothetical_protein_1098159..1098309_POSITIVE 281 95 55 71 25 pint:PI1719|3end_conserved_hypothetical_protein_1636207..1636357_POSITIVE