Origin IGS: atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta .........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 taaataagataatcaacaataaaaggttttggaaacttctccaaaaccttttattatttcaccttataaagaatataaaccgtataaacatactgaaatgttaaaattttaaatatttaaaagggctaagtaagaataaagctgttattagttaattattgtataataaaaatctaataataccctcttctgttatttaatgataaaaacacgctcttacctttttaaaaacacattcgattttataaaaaagccgtaactttacaccaaacgctataaaccaaaacctacctaagagcagttacat Mask Tandem Repeat Region ================================================ atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta Find is-nt database================================================ Query_seq: PI0429:PI0430|PI0429:PI0430:hypothetical protein:periplasmic protease; MdsD protein:->->:399663..399969 307 atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0429:PI0430|PI0429:PI0430:hypothetical protein:periplasmic protease; MdsD protein:->->:399663..399969 307 atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0429:PI0430|PI0429:PI0430:hypothetical protein:periplasmic protease; MdsD protein:->->:399663..399969 307 atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 7 End: 108 ...... M L L G R F W F I A F G V K L R L F Y K I E C V F K K V R A C F Y H ....................................................................................................................................................................................................... Protein_Len: 31 Strand: - Start: 207 End: 299 .............................................................................................................................................................................................................. C K L I N I R N I N K I L H F L L L N Q L L K W F R K N N I M ........ atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta 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: 85 Start: 251 End: 280 ..........................................................................................................................................................................................................................................................TTTGGAAACTTCTCCAAAACCTTTTATTAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.4 Tail_Score: -3.59079 Start: 252 End: 291 Full_Region: CTTTATAAGGTGAAA TAATAAAAGGTTTTGGAG AAGT TTCCAAAACCTTTTATTG TTGATTATCTTATTT ...........................................................................................................................................................................................................................................................TAATAAAAGGTTTTGGAGAAGTTTCCAAAACCTTTTATTG................ TransTerm Strand: + Conf: 100 HP_score: -14.9 Tail_Score: -3.89704 Start: 255 End: 288 Full_Region: TATAAGGTGAAATAA TAAAAGGTTTTGGAG AAGT TTCCAAAACCTTTTA TTGTTGATTATCTTA ..............................................................................................................................................................................................................................................................TAAAAGGTTTTGGAGAAGTTTCCAAAACCTTTTA................... TransTerm Strand: + Conf: 100 HP_score: -10.4 Tail_Score: -4.95167 Start: 260 End: 283 Full_Region: GGTGAAATAATAAAA GGTTTTGGAG AAGT TTCCAAAACC TTTTATTGTTGATTA ...................................................................................................................................................................................................................................................................GGTTTTGGAGAAGTTTCCAAAACC........................ Find igs database================================================ Query_seq: PI0429:PI0430|PI0429:PI0430:hypothetical protein:periplasmic protease; MdsD protein:->->:399663..399969 307 atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta Intra-Species Hit: Count: 1 Min: 1 Max: 307 Len: 307 Subject: pint_PI0429_PI0430|hypothetical protein:periplasmic protease; MdsD protein|POSITIVE:POSITIVE|[399663,399969]|307 HSP 1 e-value: 1.0E-173 bit: 609.0 Len: 307 Query Start:1 Query End:307 Subject Strand: POSITIVE Subject Start: 1 Subject End: 307 atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta atgtaactgctcttaggtaggttttggtttatagcgtttggtgtaaagttacggcttttttataaaatcgaatgtgtttttaaaaaggtaagagcgtgtttttatcattaaataacagaagagggtattattagatttttattatacaataattaactaataacagctttattcttacttagcccttttaaatatttaaaattttaacatttcagtatgtttatacggtttatattctttataaggtgaaataataaaaggttttggagaagtttccaaaaccttttattgttgattatcttattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUAACUGCUCUUAGGUAGGUUUUGGUUUAUAGCGUUUGGUGUAAAGUUACGGCUUUUUUAUAAAAUCGAAUGUGUUUUUAAAAAGGUAAGAGCGUGUUUUUAUCAUUAAAUAACAGAAGAGGGUAUUAUUAGAUUUUUAUUAUACAAUAAUUAACUAAUAACAGCUUUAUUCUUACUUAGCCCUUUUAAAUAUUUAAAAUUUUAACAUUUCAGUAUGUUUAUACGGUUUAUAUUCUUUAUAAGGUGAAAUAAUAAAAGGUUUUGGAGAAGUUUCCAAAACCUUUUAUUGUUGAUUAUCUUAUUUA ......(((((....))))).....((..(((((....(.(((((((..(((.(((((((((.(((((.......))))))))))))))..(((.(((((.......(((((((....((((((((.(((((((.(..(((((....)))))..).)))))))......((....))....))))))))...)))))))......)))))))).)))..))))))).).)))))..))..(((((((((((((((((((((((((((((....))))))))))))))))))))..)))))))))... (-67.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAAGAUAAUCAACAAUAAAAGGUUUUGGAAACUUCUCCAAAACCUUUUAUUAUUUCACCUUAUAAAGAAUAUAAACCGUAUAAACAUACUGAAAUGUUAAAAUUUUAAAUAUUUAAAAGGGCUAAGUAAGAAUAAAGCUGUUAUUAGUUAAUUAUUGUAUAAUAAAAAUCUAAUAAUACCCUCUUCUGUUAUUUAAUGAUAAAAACACGCUCUUACCUUUUUAAAAACACAUUCGAUUUUAUAAAAAAGCCGUAACUUUACACCAAACGCUAUAAACCAAAACCUACCUAAGAGCAGUUACAU ...(((((((.......((((((((((((((((......))))))))))))))))...............((((............(((((......))))).............((((((((((.((((..((((....(.(((((((((....(((((....)))))....))))))))).)...)))).(((((....))))).........)))))))))))))).....)))).))))))).........((((((...........(((.....................))))))))).. (-49.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 80 32 205 151 pint:PI0435|5end_30S_ribosomal_protein_S21_406997..407227_POSITIVE 298 60 27 147 112 pint:PI1737|5end_glycyl-tRNA_synthetase_1657766..1657996_POSITIVE 288 80 34 215 165 pint:PI2003|5end_hypothetical_protein_1960823..1961053_POSITIVE 288 80 34 54 4 pint:PI2002|5end_hypothetical_protein_1960662..1960892_POSITIVE 286 45 7 181 143 pint:PI0026|5end_two-component_system_response_regulator_29756..29986_POSITIVE 284 80 34 54 4 pint:PI1601|5end_hypothetical_protein_1530282..1530512_POSITIVE 277 49 1 115 61 pint:PI0425|5end_hypothetical_protein_389454..389684_POSITIVE 268 80 34 54 4 pint:PI1076|5end_hypothetical_protein_998893..999123_POSITIVE 258 46 6 181 142 pint:PI0309|5end_hypothetical_protein_291503..291733_POSITIVE 254 268 226 63 29 pint:PI1869|5end_hypothetical_protein_1815131..1815361_POSITIVE 250 60 41 20 1 pint:PI1868|5end_hypothetical_protein_1814638..1814868_POSITIVE 250 72 31 186 145 pint:PI0969|5end_30S_ribosomal_protein_S16_896627..896857_POSITIVE 247 60 16 216 181 pint:PI1830|5end_conserved_hypothetical_protein_1769439..1769669_POSITIVE 246 57 12 226 177 pint:PI0601|5end_hypothetical_protein_548758..548988_POSITIVE 244 70 27 70 34 pint:PI2146|5end_prolipoprotein_diacylglyceryl_transferase_2092402..2092632_POSITIVE 240 275 238 116 83 pint:PI2128|5end_hypothetical_protein_2076512..2076742_POSITIVE 240 46 1 68 21 pint:PI1635|5end_hypothetical_protein_1553948..1554178_POSITIVE 240 48 5 157 105 pint:PI0213|5end_conserved_hypothetical_protein_207065..207295_POSITIVE 240 59 16 186 147 pint:PI0138|5end_hypothetical_protein_131082..131312_POSITIVE 238 60 15 208 154 pint:PI1870|5end_hypothetical_protein_1815302..1815532_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 80 34 146 96 pint:PI1601|3end_hypothetical_protein_1530454..1530604_POSITIVE 283 80 34 110 68 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE 283 45 1 66 20 pint:PI0047|3end_phosphomethylpyrimidine_kinase_46781..46931_POSITIVE 268 80 34 146 96 pint:PI1076|3end_hypothetical_protein_999065..999215_POSITIVE 263 57 11 126 74 pint:PI2044|3end_hypothetical_protein_1997351..1997501_POSITIVE 259 80 34 96 46 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 250 72 31 125 84 pint:PI0968|3end_hypothetical_protein_896646..896796_POSITIVE 247 60 16 136 101 pint:PI1829|3end_hypothetical_protein_1769439..1769589_POSITIVE 247 48 7 136 83 pint:PI1820|3end_hypothetical_protein_1760377..1760527_POSITIVE 247 60 16 114 79 pint:PI1814|3end_hypothetical_protein_1753233..1753383_POSITIVE 245 56 21 103 63 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 240 59 11 114 63 pint:PI0761|3end_hypothetical_protein_696348..696498_POSITIVE 237 55 15 53 2 pint:PI1662|3end_hypothetical_protein_1577241..1577391_POSITIVE 235 79 32 146 95 pint:PI0347|3end_hypothetical_protein_321655..321805_POSITIVE 233 65 26 146 106 pint:PI1140|3end_ABC_transporter,_ATP-binding_protein_1069417..1069567_POSITIVE 233 54 16 151 109 pint:PI0747|3end_possible_mobilization_protein_676702..676852_POSITIVE 232 59 16 68 24 pint:PI0251|3end_hypothetical_protein_247810..247960_POSITIVE 231 55 19 41 12 pint:PI1394|3end_glutamate_formiminotransferase_1315862..1316012_POSITIVE 231 74 34 82 36 pint:PI0624|3end_hypothetical_protein_574471..574621_POSITIVE 230 60 16 114 79 pint:PI0689|3end_hypothetical_protein_625877..626027_POSITIVE