Origin IGS: accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcacaaaagtaaaaataaaatggcagaataaagaaaaatacctatataaaatacacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag .........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 ctcttatttgtaatagtattatgcattgcaaagttacgaaaatatattgaattgctaaaataaaataactatttattaaagtttttaatccataaaaatgcgctgaaagttgtatcggaatgttgtaaaaacagatataaaaggtagaaaatgtcgtgaaatcgtacaatattcgtgtacttctctgtaaaataaacgaatagttgtgtattttatataggtatttttctttattctgccattttatttttacttttgtgaaataaaaagctaacaagattataactattttatgagagtaggattatttattccgtgttatgtcgatgcattgtatccagaggtcggt Mask Tandem Repeat Region ================================================ accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcacaaaagtaaaaataaaatggcagaataaagaaaaatacctatataaaatacacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag Find is-nt database================================================ Query_seq: PI1335:PI1336|PI1335:PI1336:Fe-S oxidoreductase:dTDP-4-dehydrorhamnose 3,5-epimerase:->->:1253630..1253978 349 accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcacaaaagtaaaaataaaatggcagaataaagaaaaatacctatataaaatacacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1335:PI1336|PI1335:PI1336:Fe-S oxidoreductase:dTDP-4-dehydrorhamnose 3,5-epimerase:->->:1253630..1253978 349 accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcacaaaagtaaaaataaaatggcagaataaagaaaaatacctatataaaatacacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1335:PI1336|PI1335:PI1336:Fe-S oxidoreductase:dTDP-4-dehydrorhamnose 3,5-epimerase:->->:1253630..1253978 349 accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcacaaaagtaaaaataaaatggcagaataaagaaaaatacctatataaaatacacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcacaaaagtaaaaataaaatggcagaataaagaaaaatacctatataaaatacacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 116 End: 262 ................................................................................................................... M K K N T Y I K Y T T I R L F Y R E V H E Y C T I S R H F L P F I S V F T T F R Y N F Q R I F M D ....................................................................................... Protein_Len: 33 Strand: + Start: 180 End: 278 ................................................................................................................................................................................... M V R F H D I F Y L L Y L F L Q H S D T T F S A F L W I K N F N K ....................................................................... Protein_Len: 60 Strand: + Start: 61 End: 348 ............................................................ M V I I L L A F Y F T K V K I K W Q N K E K Y L Y K I H N Y S F I L Q R S T R I L Y D F T T F S T F Y I C F Y N I P I Q . accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcacaaaagtaaaaataaaatggcagaataaagaaaaatacctatataaaatacacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag 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================================================ accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcacaaaagtaaaaataaaatggcagaataaagaaaaatacctatataaaatacacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -3.6 Tail_Score: -3.39668 Start: 148 End: 180 Full_Region: TATAAAATACACAAC TATTCGTTTATTTT ACAGA GAAGTACACGAATA TTGTACGATTTCACG ...................................................................................................................................................TATTCGTTTATTTTACAGAGAAGTACACGAATA......................................................................................................................................................................... TransTerm Strand: - Conf: 45 HP_score: -2.3 Tail_Score: -3.59698 Start: 170 End: 186 Full_Region: aaatgtcgtgaaatc gtaca atattcg tgtac ttctctgtaaaataa .........................................................................................................................................................................gtacaatattcgtgtac................................................................................................................................................................... Find igs database================================================ Query_seq: PI1335:PI1336|PI1335:PI1336:Fe-S oxidoreductase:dTDP-4-dehydrorhamnose 3,5-epimerase:->->:1253630..1253978 349 accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcacaaaagtaaaaataaaatggcagaataaagaaaaatacctatataaaatacacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag Intra-Species Hit: Count: 1 Min: 1 Max: 349 Len: 349 Subject: pint_PI1335_PI1336|Fe-S oxidoreductase:dTDP-4-dehydrorhamnose 3,5-epimerase|POSITIVE:POSITIVE|[1253630,1253978]|349 HSP 1 e-value: 1.0E-114 bit: 412.0 Len: 208 Query Start:142 Query End:349 Subject Strand: POSITIVE Subject Start: 142 Subject End: 349 .............................................................................................................................................cacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag .............................................................................................................................................cacaactattcgtttattttacagagaagtacacgaatattgtacgatttcacgacattttctaccttttatatctgtttttacaacattccgatacaactttcagcgcatttttatggattaaaaactttaataaatagttattttattttagcaattcaatatattttcgtaactttgcaatgcataatactattacaaataagag HSP 2 e-value: 5.0E-45 bit: 182.0 Len: 92 Query Start:1 Query End:92 Subject Strand: POSITIVE Subject Start: 1 Subject End: 92 accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcac................................................................................................................................................................................................................................................................. accgacctctggatacaatgcatcgacataacacggaataaataatcctactctcataaaatagttataatcttgttagctttttatttcac................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGACCUCUGGAUACAAUGCAUCGACAUAACACGGAAUAAAUAAUCCUACUCUCAUAAAAUAGUUAUAAUCUUGUUAGCUUUUUAUUUCACAAAAGUAAAAAUAAAAUGGCAGAAUAAAGAAAAAUACCUAUAUAAAAUACACAACUAUUCGUUUAUUUUACAGAGAAGUACACGAAUAUUGUACGAUUUCACGACAUUUUCUACCUUUUAUAUCUGUUUUUACAACAUUCCGAUACAACUUUCAGCGCAUUUUUAUGGAUUAAAAACUUUAAUAAAUAGUUAUUUUAUUUUAGCAAUUCAAUAUAUUUUCGUAACUUUGCAAUGCAUAAUACUAUUACAAAUAAGAG .(((.....))).....((((((.(.((....((((((.................((((((.(((((.........))))))))))).........((.(((((((((((((.......((((((.................((((.(((((((.((((((.....)))))).))))))))))).((......))...))))))....(((((....(((((((.........((........))....(((....)))...)))))))....)))))..))))))))))))).))............)))))).....))).)))))).................... (-48.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUAUUUGUAAUAGUAUUAUGCAUUGCAAAGUUACGAAAAUAUAUUGAAUUGCUAAAAUAAAAUAACUAUUUAUUAAAGUUUUUAAUCCAUAAAAAUGCGCUGAAAGUUGUAUCGGAAUGUUGUAAAAACAGAUAUAAAAGGUAGAAAAUGUCGUGAAAUCGUACAAUAUUCGUGUACUUCUCUGUAAAAUAAACGAAUAGUUGUGUAUUUUAUAUAGGUAUUUUUCUUUAUUCUGCCAUUUUAUUUUUACUUUUGUGAAAUAAAAAGCUAACAAGAUUAUAACUAUUUUAUGAGAGUAGGAUUAUUUAUUCCGUGUUAUGUCGAUGCAUUGUAUCCAGAGGUCGGU ((((...........((((.((((((((((....((((...............(((..((((((.......))))))..)))...((((((...((((((.((.(((....((((..((((((((((....(((((((............))))).))......))))))))))..)))).(((.(((((((((.((((....)))).))))))))).)))............))).)))))))).....((((((..(((((((.....................)))))))..)))))))))))).......))))...)).)))))))).))))..))))...... (-64.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 36 1 75 39 pint:PI0207|5end_conserved_hypothetical_protein_199797..200027_POSITIVE 249 185 150 91 56 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 248 264 227 179 135 pint:PI0645|5end_hypothetical_protein_586419..586649_POSITIVE 248 264 227 158 114 pint:PI0643|5end_hypothetical_protein_586398..586628_POSITIVE 246 37 5 80 40 pint:PI0008|5end_exoribonuclease_II_(ribonuclease_II)_7238..7468_POSITIVE 246 37 5 41 1 pint:PI0006|5end_hypothetical_protein_7199..7429_POSITIVE 243 229 183 220 177 pint:PI2134|5end_hypothetical_protein_2082269..2082499_POSITIVE 241 334 295 225 185 pint:PI0858|5end_carbamyl_phosphate_synthase,_large_subunit_790093..790323_POSITIVE 233 209 173 78 33 pint:PI2053|5end_conserved_hypothetical_protein;_possible_outer_membrane_receptor_protein_2010673..2010903_POSITIVE 232 38 3 47 10 pint:PI1039|5end_conserved_hypothetical_protein_957721..957951_POSITIVE 229 212 184 178 147 pint:PI1663|5end_hypothetical_protein_1577127..1577357_POSITIVE 226 260 217 195 139 pint:PI1048|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_966277..966507_POSITIVE 226 189 143 92 49 pint:PI0397|5end_conserved_hypothetical_protein_362406..362636_POSITIVE 225 200 157 154 98 pint:PI0471|5end_50S_ribosomal_protein_L24_437736..437966_POSITIVE 225 50 3 33 1 pint:PI0016|5end_magnesium_chelatase,_subunit_ChlI_20191..20421_POSITIVE 224 260 215 80 28 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 223 219 173 177 136 pint:PI0874|5end_conserved_hypothetical_protein_808978..809208_POSITIVE 222 270 229 51 4 pint:PI1046|5end_hypothetical_protein_965792..966022_POSITIVE 222 250 207 218 162 pint:PI0426|5end_conserved_hypothetical_protein_389345..389575_POSITIVE 218 249 201 194 138 pint:PI0984|5end_hypothetical_protein_909936..910166_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 36 1 54 18 pint:PI0206|3end_TPR-repeat-containing_protein_199856..200006_POSITIVE 246 37 5 62 22 pint:PI0007|3end_hypothetical_protein_7300..7450_POSITIVE 231 252 214 116 80 pint:PI0191|3end_O-methyltransferase_181785..181935_POSITIVE 225 200 157 151 95 pint:PI0470|3end_50S_ribosomal_protein_L14_437813..437963_POSITIVE 223 219 173 75 34 pint:PI0873|3end_conserved_hypothetical_protein;_possible_permease_808956..809106_POSITIVE 223 229 181 127 76 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 222 198 153 141 83 pint:PI1069|3end_hypothetical_protein_988458..988608_POSITIVE 215 36 9 115 94 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 214 248 203 138 94 pint:PI0565|3end_hypothetical_protein_511657..511807_POSITIVE 213 246 203 145 99 pint:PI1494|3end_conserved_hypothetical_protein_1413968..1414118_POSITIVE 211 37 1 119 85 pint:PI0782|3end_beta-lactamase_induction_signal_transducer,_AmpG_protein_721927..722077_POSITIVE 209 215 188 119 90 pint:PI0813|3end_conserved_hypothetical_protein_752938..753088_POSITIVE 208 218 183 122 80 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 207 250 201 105 58 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 206 327 290 94 57 pint:PI1562|3end_methyltransferase_1480449..1480599_POSITIVE 205 44 8 49 4 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 205 260 215 114 69 pint:PI2047|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diamino_pimelate--D-alanyl-D-alanyl_ligase_2000706..2000856_POSITIVE 205 261 226 94 52 pint:PI0536|3end_hypothetical_protein_492623..492773_POSITIVE 203 115 73 128 91 pint:PI0491|3end_hypothetical_protein_451227..451377_POSITIVE 203 276 240 127 95 pint:PI0036|3end_glutathione_peroxidase_39289..39439_POSITIVE