Origin IGS: attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaaacccgaaacacgtaacaaaacaacgctatttactgcaacggagttactgtatcagtgatataaggtaggttacggcaaatggaataataaagttacagcaacactacctgcccaatagcagtttcaacggtgatgaccatggggaaacgaaagggtaggagaacgctgaaaacaataaggaagtcgtcttggtagaaagtgccaaggcggcttttttgtttgcatcagaaagtattggtgttcgctaaagaataccttttaatgctgcaaaaacggattcggtagtaat Mask Tandem Repeat Region ================================================ attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta Find is-nt database================================================ Query_seq: PI1244:PI1246|PI1244:PI1246:hypothetical protein:conserved hypothetical protein; possible lipoprotein:->->:1169237..1169531 295 attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1244:PI1246|PI1244:PI1246:hypothetical protein:conserved hypothetical protein; possible lipoprotein:->->:1169237..1169531 295 attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1244:PI1246|PI1244:PI1246:hypothetical protein:conserved hypothetical protein; possible lipoprotein:->->:1169237..1169531 295 attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 62 End: 163 ............................................................. M M Q T K K P P W H F L P R R L P Y C F Q R S P T L S F P H G H H R .................................................................................................................................... Protein_Len: 43 Strand: + Start: 55 End: 183 ...................................................... M L S D A N K K A A L A L S T K T T S L L F S A F S Y P F V S P W S S P L K L L L G R ................................................................................................................ attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta 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================================================ attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.6 Tail_Score: -5.65927 Start: 79 End: 107 Full_Region: gaaaacaataaggaa gtcgtcttggta gaaag tgccaaggcggc ttttttgtttgcatc ..............................................................................gtcgtcttggtagaaagtgccaaggcggc............................................................................................................................................................................................ Find igs database================================================ Query_seq: PI1244:PI1246|PI1244:PI1246:hypothetical protein:conserved hypothetical protein; possible lipoprotein:->->:1169237..1169531 295 attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta Intra-Species Hit: Count: 1 Min: 1 Max: 295 Len: 295 Subject: pint_PI1244_PI1246|hypothetical protein:conserved hypothetical protein; possible lipoprotein|POSITIVE:POSITIVE|[1169237,1169531]|295 HSP 1 e-value: 1.0E-166 bit: 585.0 Len: 295 Query Start:1 Query End:295 Subject Strand: POSITIVE Subject Start: 1 Subject End: 295 attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta attactaccgaatccgtttttgcagcattaaaaggtattctttagcgaacaccaatactttctgatgcaaacaaaaaagccgccttggcactttctaccaagacgacttccttattgttttcagcgttctcctaccctttcgtttccccatggtcatcaccgttgaaactgctattgggcaggtagtgttgctgtaactttattattccatttgccgtaacctaccttatatcactgatacagtaactccgttgcagtaaatagcgttgttttgttacgtgtttcgggtttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUACUACCGAAUCCGUUUUUGCAGCAUUAAAAGGUAUUCUUUAGCGAACACCAAUACUUUCUGAUGCAAACAAAAAAGCCGCCUUGGCACUUUCUACCAAGACGACUUCCUUAUUGUUUUCAGCGUUCUCCUACCCUUUCGUUUCCCCAUGGUCAUCACCGUUGAAACUGCUAUUGGGCAGGUAGUGUUGCUGUAACUUUAUUAUUCCAUUUGCCGUAACCUACCUUAUAUCACUGAUACAGUAACUCCGUUGCAGUAAAUAGCGUUGUUUUGUUACGUGUUUCGGGUUUCUUA .......(((((.(((((((((..((((((.((((((((..............)))))))).))))))...)))))..(((.....))).........(((((((((....(((((((..((((.(........(((....(((((...(((((....))))).))))).......))).((((((.(((((.((((..............)))).))))))))))).....).)))).))))))).......((........)))))))))))..))).).)))))........ (-66.78) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAACCCGAAACACGUAACAAAACAACGCUAUUUACUGCAACGGAGUUACUGUAUCAGUGAUAUAAGGUAGGUUACGGCAAAUGGAAUAAUAAAGUUACAGCAACACUACCUGCCCAAUAGCAGUUUCAACGGUGAUGACCAUGGGGAAACGAAAGGGUAGGAGAACGCUGAAAACAAUAAGGAAGUCGUCUUGGUAGAAAGUGCCAAGGCGGCUUUUUUGUUUGCAUCAGAAAGUAUUGGUGUUCGCUAAAGAAUACCUUUUAAUGCUGCAAAAACGGAUUCGGUAGUAAU ........(((((...((((((...((........((((((..((((.....))))..))))))......))..)))))).................(((.(((((...((.(((((((.......(((((..((((....)))..)..)))))....))))))))).((.((((....(((((((((((((((((((((.....)))))))))))))))))))))....))))...))...(((((((......)))))))......)))))....)))...)))))....... (-89.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 492 109 69 205 168 pint:PI1224|5end_sensor_histidine_kinase_and_response_regulator_1144574..1144804_POSITIVE 372 109 65 164 119 pint:PI1230|5end_probable_metallo-beta-lactamase_family_protein_1151840..1152070_POSITIVE 361 188 141 177 123 pint:PI1083|5end_TPR-repeat-containing_protein_1001975..1002205_POSITIVE 330 130 81 200 159 pint:PI0242|5end_hypothetical_protein_240007..240237_POSITIVE 329 142 105 228 180 pint:PI0514|5end_possible_cell_filamentation_protein_472408..472638_POSITIVE 327 190 141 197 146 pint:PI1704|5end_50S_ribosomal_protein_L32_1621418..1621648_POSITIVE 326 195 157 147 106 pint:PI0746|5end_hypothetical_protein_675971..676201_POSITIVE 322 290 241 137 89 pint:PI1499|5end_hypothetical_protein_1419960..1420190_POSITIVE 321 218 172 91 31 pint:PI1399|5end_hypothetical_protein_1320573..1320803_POSITIVE 319 180 134 62 13 pint:PI0492|5end_hypothetical_protein_451701..451931_POSITIVE 318 216 175 194 150 pint:PI1947|5end_hypothetical_protein_1902534..1902764_POSITIVE 318 189 147 149 100 pint:PI1443|5end_conserved_hypotehtical_protein;_possible_tonB-dependent_outer_membrane_receptor_1364560..1364790_POSITIVE 311 197 151 145 95 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 300 183 141 152 103 pint:PI0756|5end_50S_ribosomal_protein_L7/L12_687146..687376_POSITIVE 297 195 155 87 41 pint:PI1848|5end_hypothetical_protein_1793799..1794029_POSITIVE 288 189 145 98 55 pint:PI2109|5end_surface_antigen_BspA_2060553..2060783_POSITIVE 287 267 227 92 48 pint:PI0553|5end_recombination_protein_503344..503574_POSITIVE 285 162 122 198 155 pint:PI1635|5end_hypothetical_protein_1553948..1554178_POSITIVE 285 108 61 51 1 pint:PI0202|5end_DNA_helicase_191753..191983_POSITIVE 284 182 141 100 51 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 130 81 149 108 pint:PI0241|3end_possible_tetracycline_resistance_element_/mobilization_regulatory_protein_240036..240186_POSITIVE 329 142 105 111 63 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 324 110 62 63 14 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE 322 290 241 85 37 pint:PI1498|3end_probable_membrane_associated_lipoprotein_1419988..1420138_POSITIVE 321 105 62 73 27 pint:PI1499|3end_hypothetical_protein_1420180..1420330_POSITIVE 321 218 172 110 50 pint:PI1398|3end_probable_imidazolonepropionase_1320672..1320822_POSITIVE 313 127 81 146 93 pint:PI0547|3end_fructose-bisphosphate_aldolase_499466..499616_POSITIVE 311 197 151 142 92 pint:PI0830|3end_conserved_hypothetical_protein_768206..768356_POSITIVE 297 195 155 57 11 pint:PI1847|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_1793849..1793999_POSITIVE 295 218 172 101 66 pint:PI0798|3end_malonyl_CoA-acyl_carrier_protein_transacylase_736975..737125_POSITIVE 294 120 79 147 106 pint:PI0396|3end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_362396..362546_POSITIVE 293 125 81 144 99 pint:PI0444|3end_50S_ribosomal_protein_L7/L12_413390..413540_POSITIVE 293 125 81 113 68 pint:PI0445|3end_conserved_hypothetical_protein_413359..413509_POSITIVE 288 189 145 90 47 pint:PI2108|3end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2060625..2060775_POSITIVE 288 224 181 47 8 pint:PI0450|3end_hypothetical_protein_424046..424196_POSITIVE 286 289 241 105 53 pint:PI1892|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1835547..1835697_POSITIVE 283 172 131 125 91 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 283 194 159 141 96 pint:PI0928|3end_hypothetical_protein_860272..860422_POSITIVE 281 190 148 122 78 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 279 108 78 57 29 pint:PI1431|3end_conserved_hypothetical_protein_1352809..1352959_POSITIVE