Origin IGS: taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt .........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 aaatatacttttgttgtttgagcattcccgtaaatagttcctcctggagaaagggcttttgacgaagtatttattttatagcttgcttctccttttgcttctttcacccaatcactttgtgcatgcaaagtaaaaggaataaataagaatagtagtcgtaataatattttcattttagttcccataaatatacttttgttgtttgagcattcccgtaaatagttcctcctggagaaagggcttttgacgaagtattta Mask Tandem Repeat Region ================================================ taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt Find is-nt database================================================ Query_seq: PI1615:PI1616|PI1615:PI1616:hypothetical protein:hypothetical protein:->->:1542055..1542312 258 taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1615:PI1616|PI1615:PI1616:hypothetical protein:hypothetical protein:->->:1542055..1542312 258 taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1615:PI1616|PI1615:PI1616:hypothetical protein:hypothetical protein:->->:1542055..1542312 258 taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 68 End: 256 ................................................................... M F M G T K M K I L L R L L F L F I P F T L H A Q S D W V K E A K G E A S Y K I N T S S K A L S P G G T I Y G N A Q T T .. taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt 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================================================ taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1615:PI1616|PI1615:PI1616:hypothetical protein:hypothetical protein:->->:1542055..1542312 258 taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt Intra-Species Hit: Count: 1 Min: 1 Max: 258 Len: 258 Subject: pint_PI1615_PI1616|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1542055,1542312]|258 HSP 1 e-value: 1.0E-144 bit: 511.0 Len: 258 Query Start:1 Query End:258 Subject Strand: POSITIVE Subject Start: 1 Subject End: 258 taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt taaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatatttatgggaactaaaatgaaaatattattacgactactattcttatttattccttttactttgcatgcacaaagtgattgggtgaaagaagcaaaaggagaagcaagctataaaataaatacttcgtcaaaagccctttctccaggaggaactatttacgggaatgctcaaacaacaaaagtatattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUACUUCGUCAAAAGCCCUUUCUCCAGGAGGAACUAUUUACGGGAAUGCUCAAACAACAAAAGUAUAUUUAUGGGAACUAAAAUGAAAAUAUUAUUACGACUACUAUUCUUAUUUAUUCCUUUUACUUUGCAUGCACAAAGUGAUUGGGUGAAAGAAGCAAAAGGAGAAGCAAGCUAUAAAAUAAAUACUUCGUCAAAAGCCCUUUCUCCAGGAGGAACUAUUUACGGGAAUGCUCAAACAACAAAAGUAUAUUU ...((((((............(((((((.(((((((........(((..(((((..........(((((.(((((..........))))).)))))...................(((((.((..((((((((......))))))))..))))))).).))))...(..((((..................))))..).....)))))))))).)))))))........(((....))).........)))))).... (-45.97) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUACUUUUGUUGUUUGAGCAUUCCCGUAAAUAGUUCCUCCUGGAGAAAGGGCUUUUGACGAAGUAUUUAUUUUAUAGCUUGCUUCUCCUUUUGCUUCUUUCACCCAAUCACUUUGUGCAUGCAAAGUAAAAGGAAUAAAUAAGAAUAGUAGUCGUAAUAAUAUUUUCAUUUUAGUUCCCAUAAAUAUACUUUUGUUGUUUGAGCAUUCCCGUAAAUAGUUCCUCCUGGAGAAAGGGCUUUUGACGAAGUAUUUA ....(((((((.((((...((((.....((..(((.((((.((((((.((((((((....((.((((((..............)))))))).....)).)))))).)).....(((((((....)))))))...))))..((((((.((.((((...........(((........)))...........)))).)).)))))))))))))..)).......((((....)))).....)))).)))))))))))... (-47.69) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 178 132 61 16 pint:PI2159|5end_immunoreactive_84_kDa_antigen_PG93_2105267..2105497_POSITIVE 294 180 134 90 50 pint:PI0451|5end_serine_proteases,__S51_group_424343..424573_POSITIVE 286 238 191 75 29 pint:PI1098|5end_conserved_hypothetical_protein_1022261..1022491_POSITIVE 279 238 191 158 120 pint:PI1824|5end_ThiJ/PfpI_family_protein_1764479..1764709_POSITIVE 276 238 194 212 162 pint:PI1602|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1531025..1531255_POSITIVE 269 35 5 34 1 pint:PI1598|5end_phosphate_ABC_transporter,_phosphate-binding_component_1526646..1526876_POSITIVE 268 146 101 66 13 pint:PI0126|5end_conserved_hypothetical_protein_117925..118155_POSITIVE 264 169 124 89 40 pint:PI0786|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_723240..723470_POSITIVE 262 177 135 53 10 pint:PI0277|5end_hypothetical_protein_264980..265210_POSITIVE 261 239 192 230 182 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 258 180 133 67 27 pint:PI0608|5end_isochorismate_synthase_555487..555717_POSITIVE 256 177 132 89 46 pint:PI1495|5end_conserved_hypothetical_protein_1414432..1414662_POSITIVE 255 182 141 215 159 pint:PI1641|5end_hypothetical_protein_1558495..1558725_POSITIVE 255 48 7 66 22 pint:PI0376|5end_conserved_hypothetical_protein_346417..346647_POSITIVE 254 178 139 71 29 pint:PI1529|5end_cytosine/adenosine_deaminase_1449887..1450117_POSITIVE 254 176 131 221 164 pint:PI0156|5end_conserved_hypothetical_protein_148716..148946_POSITIVE 254 178 135 225 168 pint:PI0032|5end_hypothetical_protein_36085..36315_POSITIVE 250 183 142 94 48 pint:PI0495|5end_conserved_hypothetical_protein_454872..455102_POSITIVE 250 183 142 85 39 pint:PI0494|5end_hypothetical_protein_454863..455093_POSITIVE 249 178 133 187 138 pint:PI0884|5end_hypothetical_protein_817302..817532_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 178 132 61 16 pint:PI2158|3end_glycosyl_transferase,_group_2_family_protein_2105347..2105497_POSITIVE 269 197 152 81 31 pint:PI0129|3end_hypothetical_protein_121941..122091_POSITIVE 268 220 171 86 30 pint:PI1882|3end_hypothetical_protein_1826487..1826637_POSITIVE 264 169 124 72 23 pint:PI0784|3end_possible_amidase_enhancer_precursor_723303..723453_POSITIVE 259 236 192 83 45 pint:PI0645|3end_hypothetical_protein_586807..586957_POSITIVE 259 239 195 54 7 pint:PI0057|3end_conserved_hypothetical_protein_56512..56662_POSITIVE 258 180 133 48 8 pint:PI0607|3end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_lic_acid_synthase/2-oxoglutarate_decarboxylase_555548..555698_POSITIVE 256 174 132 151 111 pint:PI1089|3end_conserved_hypothetical_protein_1014040..1014190_POSITIVE 254 176 131 112 55 pint:PI0155|3end_conserved_hypothetical_protein_148687..148837_POSITIVE 250 183 142 54 8 pint:PI0493|3end_surface_antigen_BspA_454912..455062_POSITIVE 249 178 133 56 7 pint:PI0883|3end_para-aminobenzoate_synthase_component_I_817251..817401_POSITIVE 248 163 121 70 13 pint:PI1950|3end_iron-regulated_membrane_permease_1905888..1906038_POSITIVE 248 176 131 55 1 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 246 170 131 130 91 pint:PI1964|3end_conserved_hypothetical_protein_1922853..1923003_POSITIVE 243 179 131 111 69 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 242 180 133 151 110 pint:PI1723|3end_conserved_hypothetical_protein_1642133..1642283_POSITIVE 240 34 7 130 105 pint:PI0972|3end_glycine_cleavage_system_H_protein_2_899399..899549_POSITIVE 240 179 131 84 42 pint:PI0567|3end_hypothetical_protein_513055..513205_POSITIVE 239 52 18 100 64 pint:PI0201|3end_hypothetical_protein_195398..195548_POSITIVE 237 178 132 57 1 pint:PI1822|3end_ABC_transporter,_ATP-binding_/_permease_1763265..1763415_POSITIVE