Origin IGS: taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattataaaaaaatacgact .........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 agtcgtatttttttataattagttagacaaattacccccgtttgcctcatacaatgggacggaacggggacaatgtttatgaacgcttttgtcagtggtaaacgatatctttccgttcagttgcaaatataattcttttttttaagaatcacaacaatttggaatgtaaaagtgttttttcttatta Mask Tandem Repeat Region ================================================ taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattataaaaaaatacgact Find is-nt database================================================ Query_seq: PI1497:PI1498|PI1497:PI1498:LuxS protein, autoinducer AI-2 production protein:probable membrane associated lipoprotein:->->:1418380..1418566 187 taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattataaaaaaatacgact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1497:PI1498|PI1497:PI1498:LuxS protein, autoinducer AI-2 production protein:probable membrane associated lipoprotein:->->:1418380..1418566 187 taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattataaaaaaatacgact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1497:PI1498|PI1497:PI1498:LuxS protein, autoinducer AI-2 production protein:probable membrane associated lipoprotein:->->:1418380..1418566 187 taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattataaaaaaatacgact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattataaaaaaatacgact Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 62 End: 166 ............................................................. M Q L N G K I S F T T D K S V H K H C P R S V P L Y E A N G G N L S N ..................... Protein_Len: 31 Strand: + Start: 93 End: 185 ............................................................................................ M T K A F I N I V P V P S H C M R Q T G V I C L T N Y K K I R .. Protein_Len: 33 Strand: - Start: 59 End: 157 .......................................................... I Q L Q V S L Y R K G S V F A N M F M T G T G D W Q I L C V P T M .............................. taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattataaaaaaatacgact 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: 81 Start: 39 End: 68 ......................................GTTGCAAATATAATTCTTTTTTTTAAGAAT....................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattataaaaaaatacgact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.0 Tail_Score: -3.57144 Start: 35 End: 60 Full_Region: TACATTCCAAATTGT TGTGATTCTT AAAAAA AAGAATTATA TTTGCAACTGAACGG ..................................TGTGATTCTTAAAAAAAAGAATTATA............................................................................................................................... Find igs database================================================ Query_seq: PI1497:PI1498|PI1497:PI1498:LuxS protein, autoinducer AI-2 production protein:probable membrane associated lipoprotein:->->:1418380..1418566 187 taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattataaaaaaatacgact Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: pint_PI1497_PI1498|LuxS protein, autoinducer AI-2 production protein:probable membrane associated lipoprotein|POSITIVE:POSITIVE|[1418380,1418566]|187 HSP 1 e-value: 3.0E-79 bit: 295.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 taataagaaaaaacacttttacattccaaattgttgtgattcttnnnnnnnngaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattat.............. taataagaaaaaacacttttacattccaaattgttgtgattcttaaaaaaaagaattatatttgcaactgaacggaaagatatcgtttaccactgacaaaagcgttcataaacattgtccccgttccgtcccattgtatgaggcaaacgggggtaatttgtctaactaattat.............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAGAAAAAACACUUUUACAUUCCAAAUUGUUGUGAUUCUUAAAAAAAAGAAUUAUAUUUGCAACUGAACGGAAAGAUAUCGUUUACCACUGACAAAAGCGUUCAUAAACAUUGUCCCCGUUCCGUCCCAUUGUAUGAGGCAAACGGGGGUAAUUUGUCUAACUAAUUAU .....(((...(((.(((((..........((((((((((((((......))))))))))...)))).(((((((.......)))))))........))))).))).......(((..(((((((..(((.(((...))).))).)))))))..)))...))).......... (-34.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUUAGUUAGACAAAUUACCCCCGUUUGCCUCAUACAAUGGGACGGAACGGGGACAAUGUUUAUGAACGCUUUUGUCAGUGGUAAACGAUAUCUUUCCGUUCAGUUGCAAAUAUAAUUCUUUUUUUUAAGAAUCACAACAAUUUGGAAUGUAAAAGUGUUUUUUCUUAUUA .........((((((......(((((((((.(((((...))))).).))))))))....)))))).(((((((((((.((..((((.....))))..((((....((((........((((((......))))))..))))....)))).))))))))))))).......... (-35.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 155 111 140 108 pint:PI1136|5end_conserved_hypothetical_protein_1062195..1062425_POSITIVE 345 136 94 163 118 pint:PI0396|5end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_361993..362223_POSITIVE 315 160 115 178 126 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 294 160 113 95 46 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 291 150 101 201 157 pint:PI0817|5end_glycosyl_transferase,_group_1_family_protein_756861..757091_POSITIVE 289 153 114 179 135 pint:PI1477|5end_TonB-dependent_outer_membrane_receptor_1399734..1399964_POSITIVE 284 153 117 157 126 pint:PI0221|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_212356..212586_POSITIVE 283 156 116 205 152 pint:PI0122|5end_outer_membrane_protein,_ompH_family_113319..113549_POSITIVE 281 99 59 203 166 pint:PI0854|5end_MiaB-like_tRNA_modifying_enzyme_786513..786743_POSITIVE 275 148 101 229 177 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 275 148 101 62 10 pint:PI0196|5end_hypothetical_protein_188435..188665_POSITIVE 271 154 120 43 4 pint:PI1756|5end_conserved_hypothetical_protein_1682627..1682857_POSITIVE 271 150 101 145 79 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 268 154 123 107 67 pint:PI1923|5end_conserved_hypothetical_protein_1865560..1865790_POSITIVE 267 160 113 124 54 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 263 153 117 58 23 pint:PI0810|5end_hypothetical_protein_746743..746973_POSITIVE 263 153 117 53 18 pint:PI0811|5end_protease/hemagglutinin_PrtT,_streptopain_family_746738..746968_POSITIVE 262 162 122 196 150 pint:PI1749|5end_conserved_hypothetical_protein_1671039..1671269_POSITIVE 262 156 118 94 57 pint:PI0223|5end_topoisomerase_IA_218377..218607_POSITIVE 259 105 64 92 38 pint:PI0822|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_761028..761258_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 155 111 68 36 pint:PI1135|3end_hypothetical_protein_1062203..1062353_POSITIVE 290 138 91 96 49 pint:PI1884|3end_conserved_hypothetical_protein_1827457..1827607_POSITIVE 284 153 114 104 53 pint:PI0931|3end_hypothetical_protein_863073..863223_POSITIVE 284 153 117 62 31 pint:PI0220|3end_conserved_hypothetical_protein_212341..212491_POSITIVE 272 160 115 148 92 pint:PI0253|3end_conjugative_transposon_protein,_TraD_248973..249123_POSITIVE 271 150 101 135 69 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 268 153 116 151 105 pint:PI0073|3end_dihydropteroate_synthase_71785..71935_POSITIVE 267 160 113 115 45 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 267 144 101 151 109 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 267 155 114 146 105 pint:PI0407|3end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_374147..374297_POSITIVE 266 154 113 151 108 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 263 148 101 100 39 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 262 156 118 79 42 pint:PI0222|3end_conserved_hypothetical_protein_218442..218592_POSITIVE 258 144 102 78 40 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 258 160 116 58 10 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 257 163 122 83 33 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE 255 144 101 142 95 pint:PI2068|3end_hypothetical_protein_2028800..2028950_POSITIVE 253 163 123 149 108 pint:PI0287|3end_ISPg3-related_transposase_272352..272502_POSITIVE 252 152 121 145 101 pint:PI2142|3end_conserved_hypothetical_protein_2089176..2089326_POSITIVE 252 149 115 139 107 pint:PI0980|3end_conserved_hypothetical_protein_907021..907171_POSITIVE