Origin IGS: ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac .........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 gtccattacgttaccacgcatggcaaattccttgaactctttaataaaagccataagataaaattttaatcaatgctgcaagaaaacctacaatctttttcaattaacataagtcaagttatcctaccaacacatctttatttaataatgtttaatactcttttcggttgcaaatataagaacttttttgtaactttgcatacgaagagataaaaaatattacttttctcttgaaataaacttataggtaatatagtattcactttaaataaagacaa Mask Tandem Repeat Region ================================================ ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac Find is-nt database================================================ Query_seq: PI0823:PI0824|PI0823:PI0824:glyceraldehyde 3-phosphate dehydrogenase, type I:large conductance mechanosensitive channel protein:->->:763199..763476 278 ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0823:PI0824|PI0823:PI0824:glyceraldehyde 3-phosphate dehydrogenase, type I:large conductance mechanosensitive channel protein:->->:763199..763476 278 ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0823:PI0824|PI0823:PI0824:glyceraldehyde 3-phosphate dehydrogenase, type I:large conductance mechanosensitive channel protein:->->:763199..763476 278 ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 1 End: 138 M S L F K V N T I L P I S L F Q E K S N I F Y L F V C K V T K K F L Y L Q P K R V L N I I K ............................................................................................................................................ Protein_Len: 46 Strand: - Start: 69 End: 206 .................................................................... R K T H L T V F F N K Y K C G F L T N F M I L Y L H T P L I V Q S I N I S F S Q L N E Q L M ........................................................................ ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac 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: 82 Start: 0 End: 29 aTTGTCTTTATTTAAAGTGAATACTATATT......................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 20 End: 49 ...................CTTGAAATAAACTTATAGGTAATATAGTAT..................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 154 End: 183 .........................................................................................................................................................TTTTTCAATTAACATAAGTCAAGTTATCCT............................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0823:PI0824|PI0823:PI0824:glyceraldehyde 3-phosphate dehydrogenase, type I:large conductance mechanosensitive channel protein:->->:763199..763476 278 ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac Intra-Species Hit: Count: 1 Min: 1 Max: 278 Len: 278 Subject: pint_PI0823_PI0824|glyceraldehyde 3-phosphate dehydrogenase, type I:large conductance mechanosensitive channel protein|POSITIVE:POSITIVE|[763199,763476]|278 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 278 Query Start:1 Query End:278 Subject Strand: POSITIVE Subject Start: 1 Subject End: 278 ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac ttgtctttatttaaagtgaatactatattacctataagtttatttcaagagaaaagtaatattttttatctcttcgtatgcaaagttacaaaaaagttcttatatttgcaaccgaaaagagtattaaacattattaaataaagatgtgttggtaggataacttgacttatgttaattgaaaaagattgtaggttttcttgcagcattgattaaaattttatcttatggcttttattaaagagttcaaggaatttgccatgcgtggtaacgtaatggac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCUUUAUUUAAAGUGAAUACUAUAUUACCUAUAAGUUUAUUUCAAGAGAAAAGUAAUAUUUUUUAUCUCUUCGUAUGCAAAGUUACAAAAAAGUUCUUAUAUUUGCAACCGAAAAGAGUAUUAAACAUUAUUAAAUAAAGAUGUGUUGGUAGGAUAACUUGACUUAUGUUAAUUGAAAAAGAUUGUAGGUUUUCUUGCAGCAUUGAUUAAAAUUUUAUCUUAUGGCUUUUAUUAAAGAGUUCAAGGAAUUUGCCAUGCGUGGUAACGUAAUGGAC ..((((((((((((((((((((((.......................(((((.(((........))).)))))(((..((((((...((......)).......))))))..)))....))))))...)))).))))))))))))((((((.(((((.((((((....((.((........)).))..)))))).)))))))))))..............((((..(((((((....)))))))..)))).....((((((((....)))).)))).. (-52.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCCAUUACGUUACCACGCAUGGCAAAUUCCUUGAACUCUUUAAUAAAAGCCAUAAGAUAAAAUUUUAAUCAAUGCUGCAAGAAAACCUACAAUCUUUUUCAAUUAACAUAAGUCAAGUUAUCCUACCAACACAUCUUUAUUUAAUAAUGUUUAAUACUCUUUUCGGUUGCAAAUAUAAGAACUUUUUUGUAACUUUGCAUACGAAGAGAUAAAAAAUAUUACUUUUCUCUUGAAAUAAACUUAUAGGUAAUAUAGUAUUCACUUUAAAUAAAGACAA (.((((..(((....))).)))))..((..(((((.....(((((...(((.....(((.........)))...)))....(((((..........))))).)))))......)))))..))............(((((((((((....((..(((((((((((((..(((((((((((((....)))))))..))))))..))))))))......((((((((((((....))))..........)))))))).))))).)).)))))))))))... (-42.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 90 48 195 143 pint:PI0975|5end_glycine_dehydrogenase_[decarboxylating]_subunit_2_900798..901028_POSITIVE 251 268 226 183 140 pint:PI2043|5end_hypothetical_protein_1996058..1996288_POSITIVE 239 116 78 129 86 pint:PI1514|5end_tRNA_nucleotidyltransferase/poly(A)_polymerase_1432544..1432774_POSITIVE 232 130 81 179 142 pint:PI1247|5end_conserved_hypothetical_protein_1171630..1171860_POSITIVE 228 266 239 229 205 pint:PI0964|5end_conserved_hypothetical_protein_893238..893468_POSITIVE 228 266 239 189 165 pint:PI0963|5end_hypothetical_protein_893198..893428_POSITIVE 227 266 226 78 37 pint:PI1133|5end_GrpE_protein_1059662..1059892_POSITIVE 224 208 170 222 183 pint:PI0782|5end_beta-lactamase_induction_signal_transducer,_AmpG_protein_720573..720803_POSITIVE 223 262 226 58 27 pint:PI0257|5end_conjugative_transposon_protein,_TraF_249348..249578_POSITIVE 219 269 222 87 39 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 217 190 147 93 51 pint:PI0040|5end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41010..41240_POSITIVE 215 110 67 205 161 pint:PI1638|5end_conserved_hypothetical_protein_1555337..1555567_POSITIVE 214 119 79 60 19 pint:PI1005|5end_hypothetical_protein_926201..926431_POSITIVE 214 235 197 118 77 pint:PI0876|5end_hypothetical_protein_810767..810997_POSITIVE 214 266 221 168 115 pint:PI0588|5end_hypothetical_protein_535016..535246_POSITIVE 212 266 225 48 6 pint:PI1330|5end_WxcM-like,_C-terminal_family_protein_1247936..1248166_POSITIVE 212 230 184 147 108 pint:PI0837|5end_conserved_hypothetical_protein_772308..772538_POSITIVE 211 235 191 101 68 pint:PI1725|5end_hypothetical_protein_1643024..1643254_POSITIVE 211 260 230 180 148 pint:PI1335|5end_Fe-S_oxidoreductase_1252818..1253048_POSITIVE 211 159 114 189 150 pint:PI0862|5end_polysaccharide_export_outer_membrane_protein_798269..798499_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 270 238 124 100 pint:PI1999|3end_hypothetical_protein_1956668..1956818_POSITIVE 263 90 48 142 90 pint:PI0973|3end_glycine_dehydrogenase_[decarboxylating]_subunit_1_900825..900975_POSITIVE 237 268 221 107 58 pint:PI1940|3end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1897267..1897417_POSITIVE 235 270 222 110 58 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 225 210 167 131 84 pint:PI1344|3end_hypothetical_protein_1259104..1259254_POSITIVE 223 262 226 50 19 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 219 265 224 94 54 pint:PI2147|3end_GTP-binding_protein_2094407..2094557_POSITIVE 217 270 239 84 43 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 217 261 221 44 5 pint:PI0635|3end_dephospho-CoA_kinase_581690..581840_POSITIVE 217 190 147 80 38 pint:PI0039|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_41077..41227_POSITIVE 215 110 67 72 28 pint:PI1637|3end_hypothetical_protein_1555284..1555434_POSITIVE 214 155 111 150 102 pint:PI1853|3end_conserved_hypothetical_protein_1800754..1800904_POSITIVE 212 230 184 132 93 pint:PI0836|3end_conserved_hypothetical_protein_772373..772523_POSITIVE 211 270 227 145 107 pint:PI1672|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587529..1587679_POSITIVE 211 159 114 110 71 pint:PI0861|3end_glucosamine--fructose-6-phosphate_aminotransferase_(glutamine-fructose-6-phosphate_transaminase_(isomerizing))_798270..798420_POSITIVE 198 270 225 139 84 pint:PI1547|3end_hypothetical_protein_1466226..1466376_POSITIVE 197 263 221 96 55 pint:PI1077|3end_hypothetical_protein_999569..999719_POSITIVE 197 270 255 16 2 pint:PI0931|3end_hypothetical_protein_863073..863223_POSITIVE 197 209 164 79 27 pint:PI0624|3end_hypothetical_protein_574471..574621_POSITIVE 195 270 224 58 5 pint:PI2161|3end_hypothetical_protein_2108751..2108901_POSITIVE