Origin IGS: atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta .........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 tagcaaactatcatagtggtataatctaatcataaatttaaattcaaaatcttggatttaaaagaaaaaataagtaactttgcaatataaagatataaaatagcgattgtggaaagaataagcatcaatgcagatcgctacatttgggcaatccaaagagctggtcttacagagggtgactat Mask Tandem Repeat Region ================================================ atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta Find is-nt database================================================ Query_seq: PI0904:PI0905|PI0904:PI0905:conserved hypothetical protein:hypothetical protein:->->:834356..834538 183 atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0904:PI0905|PI0904:PI0905:conserved hypothetical protein:hypothetical protein:->->:834356..834538 183 atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0904:PI0905|PI0904:PI0905:conserved hypothetical protein:hypothetical protein:->->:834356..834538 183 atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 1 End: 123 M V T L C K T S S L D C P N V A I C I D A Y S F H N R Y F I S L Y C K V T Y F F F ............................................................ Protein_Len: 32 Strand: + Start: 56 End: 151 ....................................................... M M L I L S T I A I L Y L Y I A K L L I F S F K S K I L N L N L ................................ atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta 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================================================ atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0904:PI0905|PI0904:PI0905:conserved hypothetical protein:hypothetical protein:->->:834356..834538 183 atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: pint_PI0904_PI0905|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[834356,834538]|183 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta atagtcaccctctgtaagaccagctctttggattgcccaaatgtagcgatctgcattgatgcttattctttccacaatcgctattttatatctttatattgcaaagttacttattttttcttttaaatccaagattttgaatttaaatttatgattagattataccactatgatagtttgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGUCACCCUCUGUAAGACCAGCUCUUUGGAUUGCCCAAAUGUAGCGAUCUGCAUUGAUGCUUAUUCUUUCCACAAUCGCUAUUUUAUAUCUUUAUAUUGCAAAGUUACUUAUUUUUUCUUUUAAAUCCAAGAUUUUGAAUUUAAAUUUAUGAUUAGAUUAUACCACUAUGAUAGUUUGCUA ((((((.......((((..((((....)))).))))......((((((((.((.(..((.......))..).))..)))))))).(((((..((((.(((.(((((((....((((........))))....)))))))))).))))..)))))...)))))).................... (-23.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAAACUAUCAUAGUGGUAUAAUCUAAUCAUAAAUUUAAAUUCAAAAUCUUGGAUUUAAAAGAAAAAAUAAGUAACUUUGCAAUAUAAAGAUAUAAAAUAGCGAUUGUGGAAAGAAUAAGCAUCAAUGCAGAUCGCUACAUUUGGGCAAUCCAAAGAGCUGGUCUUACAGAGGGUGACUAU ..........(((((((.((................(((((((((((....)))))))))))...........(((.(((((.....))))).)))......)).)))))))........((((((..((.((((((((...(((((.....))))).))).)))))..))...)))).)).. (-34.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 83 41 79 40 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 301 53 11 86 33 pint:PI2057|5end_conserved_hypothetical_protein;_possible_metal-dependent_membrane_protease_2014939..2015169_POSITIVE 297 70 21 73 22 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 284 60 11 193 135 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 281 48 9 160 122 pint:PI0248|5end_protein_associated_with_conjugate_transformation/chromosome_partioning_246139..246369_POSITIVE 280 45 3 142 95 pint:PI1948|5end_hypothetical_protein_1903084..1903314_POSITIVE 280 81 41 168 132 pint:PI1813|5end_hypothetical_protein_1752878..1753108_POSITIVE 279 64 23 95 39 pint:PI1223|5end_conserved_hypothetical_protein_1143537..1143767_POSITIVE 277 39 1 71 38 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 276 49 10 168 120 pint:PI2109|5end_surface_antigen_BspA_2060553..2060783_POSITIVE 275 37 1 213 166 pint:PI1497|5end_LuxS_protein,_autoinducer_AI-2_production_protein_1417571..1417801_POSITIVE 274 54 13 45 3 pint:PI0817|5end_glycosyl_transferase,_group_1_family_protein_756861..757091_POSITIVE 272 45 5 55 1 pint:PI0653|5end_hypothetical_protein_596046..596276_POSITIVE 270 58 19 67 29 pint:PI2052|5end_hypothetical_protein_2008594..2008824_POSITIVE 269 63 30 183 150 pint:PI0993|5end_probable_TPR-repeat-containing_protein_917175..917405_POSITIVE 269 48 7 68 26 pint:PI0131|5end_conserved_hypothetical_protein_(possible_outer_membrane_lipoprotein)_122490..122720_POSITIVE 267 51 14 225 166 pint:PI1212|5end_shikimate_5-dehydrogenase_1130674..1130904_POSITIVE 263 43 8 226 178 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 259 64 21 223 174 pint:PI1539|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1459804..1460034_POSITIVE 259 89 41 217 162 pint:PI1505|5end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_1424922..1425152_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 88 41 109 59 pint:PI0713|3end_hypothetical_protein_650529..650679_POSITIVE 337 48 9 151 102 pint:PI0438|3end_elongation_factor_Tu_410304..410454_POSITIVE 327 83 41 70 31 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 297 70 21 60 9 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 294 56 11 113 67 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 280 81 41 64 28 pint:PI1812|3end_possible_alpha-amylase_1752854..1753004_POSITIVE 272 60 19 54 7 pint:PI1256|3end_conserved_hypothetical_protein_1178109..1178259_POSITIVE 269 63 30 150 117 pint:PI0992|3end_RNA_polymerase_sigma-70_factor_917222..917372_POSITIVE 264 80 33 44 3 pint:PI2136|3end_hypothetical_protein_2082840..2082990_POSITIVE 263 62 21 86 37 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 259 89 41 119 64 pint:PI1504|3end_non-specific_DNA-binding_protein_1424904..1425054_POSITIVE 259 87 46 128 84 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 254 58 22 70 24 pint:PI0110|3end_ABC_transport_system,_ATP-binding_protein_107920..108070_POSITIVE 252 31 5 145 111 pint:PI0653|3end_hypothetical_protein_596236..596386_POSITIVE 250 117 74 77 35 pint:PI2124|3end_excinuclease_ABC,_subunit_C_2074496..2074646_POSITIVE 250 59 11 70 8 pint:PI0400|3end_conserved_hypothetical_protein_365042..365192_POSITIVE 250 49 1 52 5 pint:PI0065|3end_conserved_hypothetical_protein_65312..65462_POSITIVE 247 50 7 92 53 pint:PI0553|3end_recombination_protein_504383..504533_POSITIVE 246 89 45 84 42 pint:PI0141|3end_glutamine_amidotransferase_involved_in_pyridoxine_biosynthesis_133308..133458_POSITIVE 245 70 23 79 40 pint:PI0728|3end_integrase_661508..661658_POSITIVE