Origin IGS: tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta .........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 tagtagtagagttgtttggatatttttcctcatctaataagttgcgttagttgttagttgcaaaagtaattatatttcattaaaatgccaaataaacaacaaataatttactattaaaccgtaatgtgttaaaaaaaagcactttacaatgtttcttaacatcgcagaatagatagtttctggattcaaaagcggagtatttgcatttttggcagttcgtatttattgttcta Mask Tandem Repeat Region ================================================ tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta Find is-nt database================================================ Query_seq: PI1511:PI1513|PI1511:PI1513:hypothetical protein:conserved hypothetical protein:->->:1430059..1430291 233 tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1511:PI1513|PI1511:PI1513:hypothetical protein:conserved hypothetical protein:->->:1430059..1430291 233 tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1511:PI1513|PI1511:PI1513:hypothetical protein:conserved hypothetical protein:->->:1430059..1430291 233 tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 8 End: 151 ....... M N T N C Q K C K Y S A F E S R N Y L F C D V K K H C K V L F F N T L R F N S K L F V V Y L A F .................................................................................. Protein_Len: 50 Strand: + Start: 12 End: 161 ........... M R T A K N A N T P L L N P E T I Y S A M L R N I V K C F F L T H Y G L I V N Y L L F I W H F N E I ........................................................................ tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 148 End: 177 ...................................................................................................................................................GTTGCAAAAGTAATTATATTTCATTAAAAT........................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1511:PI1513|PI1511:PI1513:hypothetical protein:conserved hypothetical protein:->->:1430059..1430291 233 tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: pint_PI1511_PI1513|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1430059,1430291]|233 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 233 Query Start:1 Query End:233 Subject Strand: POSITIVE Subject Start: 1 Subject End: 233 tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcnnnnnnnnaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta tagaacaataaatacgaactgccaaaaatgcaaatactccgcttttgaatccagaaactatctattctgcgatgttaagaaacattgtaaagtgcttttttttaacacattacggtttaatagtaaattatttgttgtttatttggcattttaatgaaatataattacttttgcaactaacaactaacgcaacttattagatgaggaaaaatatccaaacaactctactacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAACAAUAAAUACGAACUGCCAAAAAUGCAAAUACUCCGCUUUUGAAUCCAGAAACUAUCUAUUCUGCGAUGUUAAGAAACAUUGUAAAGUGCUUUUUUUUAACACAUUACGGUUUAAUAGUAAAUUAUUUGUUGUUUAUUUGGCAUUUUAAUGAAAUAUAAUUACUUUUGCAACUAACAACUAACGCAACUUAUUAGAUGAGGAAAAAUAUCCAAACAACUCUACUACUA ((((..(((((....(((.(((((((...(((((((....(((.((((((((((((........)))))...((((((((((((((....))))...))))))))))......))))))).)))....)))))))......))))))).)))..................((((..............)))).)))))......(((......))).......))))...... (-35.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAGUAGAGUUGUUUGGAUAUUUUUCCUCAUCUAAUAAGUUGCGUUAGUUGUUAGUUGCAAAAGUAAUUAUAUUUCAUUAAAAUGCCAAAUAAACAACAAAUAAUUUACUAUUAAACCGUAAUGUGUUAAAAAAAAGCACUUUACAAUGUUUCUUAACAUCGCAGAAUAGAUAGUUUCUGGAUUCAAAAGCGGAGUAUUUGCAUUUUUGGCAGUUCGUAUUUAUUGUUCUA ((((((((((.((((((((.((((((....((.(((((.......))))).)).(((((((....))))))).........))))))))))))))...........))))))))))...((.(((.(((((((((...(((...(((..(((((......(((.(((((........))))))))....)))))..)))..))).)))))))))))))).............. (-41.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 70 29 128 87 pint:PI1604|5end_hypothetical_protein_1534017..1534247_POSITIVE 247 47 3 176 143 pint:PI1048|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_966277..966507_POSITIVE 246 88 41 84 37 pint:PI0610|5end_conserved_hypothetical_protein_557403..557633_POSITIVE 238 55 20 219 186 pint:PI0991|5end_conserved_hypothetical_protein_915309..915539_POSITIVE 237 175 132 229 197 pint:PI0737|5end_hypothetical_protein_671182..671412_POSITIVE 237 76 39 73 38 pint:PI0729|5end_integrase_661428..661658_POSITIVE 233 69 21 54 9 pint:PI0257|5end_conjugative_transposon_protein,_TraF_249348..249578_POSITIVE 232 62 21 219 181 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 225 82 58 214 192 pint:PI0167|5end_hypothetical_protein_163164..163394_POSITIVE 223 156 113 178 134 pint:PI2038|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1990463..1990693_POSITIVE 222 57 30 109 84 pint:PI1664|5end_conserved_hypothetical_protein_1577285..1577515_POSITIVE 222 57 30 109 84 pint:PI0370|5end_conserved_hypothetical_protein_340453..340683_POSITIVE 221 94 62 41 1 pint:PI1246|5end_conserved_hypothetical_protein;_possible_lipoprotein_1169392..1169622_POSITIVE 219 54 13 205 169 pint:PI0496|5end_heat_shock_protein_hsp70_(chaperone_protein_dnaK)_456632..456862_POSITIVE 218 205 161 128 88 pint:PI0558|5end_probable_transcriptional_regulator,_TetR_family_507036..507266_POSITIVE 215 156 112 61 19 pint:PI1219|5end_UDP-N-acetylglucosamine_acyltransferase_1138529..1138759_POSITIVE 215 54 18 82 39 pint:PI0593|5end_NAD-specific_glutamate_dehydrogenase_542967..543197_POSITIVE 214 70 21 76 29 pint:PI1021|5end_conserved_hypothetical_protein;_possible_methyltransferase_938985..939215_POSITIVE 214 55 28 78 49 pint:PI0659|5end_hypothetical_protein_603203..603433_POSITIVE 214 55 28 220 191 pint:PI0196|5end_hypothetical_protein_188435..188665_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 73 39 39 5 pint:PI1603|3end_hypothetical_protein_1534005..1534155_POSITIVE 237 76 39 73 38 pint:PI0728|3end_integrase_661508..661658_POSITIVE 233 69 21 46 1 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 232 136 93 96 51 pint:PI0889|3end_pyruvate_kinase_820355..820505_POSITIVE 230 210 183 40 8 pint:PI1454|3end_chromosomal_replication_initiator_protein,_DnaA_1378141..1378291_POSITIVE 223 49 1 125 72 pint:PI1879|3end_uracil_phosphoribosyltransferase_1821245..1821395_POSITIVE 223 178 131 66 25 pint:PI1429|3end_L-aspartate_oxidase_1349325..1349475_POSITIVE 222 57 30 91 66 pint:PI1663|3end_hypothetical_protein_1577347..1577497_POSITIVE 220 97 59 137 102 pint:PI1942|3end_hypothetical_protein_1901269..1901419_POSITIVE 215 156 112 49 7 pint:PI1218|3end_UDP-3-O-acyl-N-acetylglucosamine_deacetylase_1138597..1138747_POSITIVE 213 71 37 136 94 pint:PI0225|3end_conserved_hypothetical_protein_222759..222909_POSITIVE 210 218 177 49 16 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE 209 104 67 51 20 pint:PI1671|3end_hypothetical_protein_1586653..1586803_POSITIVE 208 47 19 130 102 pint:PI0139|3end_pyridoxine_biosynthesis_protein_132724..132874_POSITIVE 207 79 52 59 25 pint:PI0810|3end_hypothetical_protein_747026..747176_POSITIVE 207 79 52 141 107 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE 207 56 16 107 61 pint:PI0435|3end_30S_ribosomal_protein_S21_407265..407415_POSITIVE 203 55 11 69 26 pint:PI1608|3end_possible_Na+/H+_anti-porter_1536300..1536450_POSITIVE 202 207 164 71 29 pint:PI0519|3end_5'-nucleotidase/2',3'-cyclic_phosphodiesterase_478809..478959_POSITIVE 202 56 13 43 2 pint:PI0186|3end_hypothetical_protein_178003..178153_POSITIVE