Origin IGS: taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaatatttctctacacgtaaagaaatatttatttacgtgtaaataatttatgcgaacctgagttcgatataagaaatttctcaaatatattatctataaggcacttagagatttataaaccccaaaataaagaaataatcttgtgattcgagtatttattaccacttaaaaggattatagtgagctattttttctaatcaagtccattaaaaaagaattgataataacttaatatgcttataatcacaagaaacggaatattttcatttaattcttatatcgaactcacgttatgcgattgcgtattttgttgattgtgccattgttgtaacaagagaaaaaggaacgctaaggattta Mask Tandem Repeat Region ================================================ taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta Find is-nt database================================================ Query_seq: PI0310:PI0312|PI0310:PI0312:outer membrane protein:hypothetical protein:->->:294371..294730 360 taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0310:PI0312|PI0310:PI0312:outer membrane protein:hypothetical protein:->->:294371..294730 360 taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0310:PI0312|PI0310:PI0312:outer membrane protein:hypothetical protein:->->:294371..294730 360 taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 267 End: 359 .......................................................................................................................................................................................................................................................................... M I Y L R N F L Y R T Q V R I N Y L H V N K Y F F T C R E I F . Protein_Len: 39 Strand: - Start: 217 End: 333 ........................................................................................................................................................................................................................ L I I E K N Q P K Y I E L H R I S L I N S F N R I D F E P E C L N N V R L Y M ........................... taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta 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: 84 Start: 110 End: 139 .............................................................................................................CTTGTGATTATAAGCATATTAAGTTATTAT............................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0310:PI0312|PI0310:PI0312:outer membrane protein:hypothetical protein:->->:294371..294730 360 taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta Intra-Species Hit: Count: 2 Min: 1 Max: 360 Len: 360 Subject: pint_PI0310_PI0312|outer membrane protein:hypothetical protein|POSITIVE:POSITIVE|[294371,294730]|360 HSP 1 e-value: 0.0 bit: 714.0 Len: 360 Query Start:1 Query End:360 Subject Strand: POSITIVE Subject Start: 1 Subject End: 360 taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta taaatccttagcgttcctttttctcttgttacaacaatggcacaatcaacaaaatacgcaatcgcataacgtgagttcgatataagaattaaatgaaaatattccgtttcttgtgattataagcatattaagttattatcaattcttttttaatggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactcaggttcgcataaattatttacacgtaaataaatatttctttacgtgtagagaaatattta Subject: pint_PI0515_PI0516|conserved hypothetical protein:ferredoxin, 4Fe-4S|POSITIVE:POSITIVE|[475492,476003]|512 HSP 1 e-value: 8.0E-69 bit: 262.0 Len: 237 Query Start:65 Query End:301 Subject Strand: NEGATIVE Subject Start: 150 Subject End: 389 ................................................................cataacgtgagttcgatataagaattaaatgaaaa-tattccgtttcttgt-gattataagcatattaagttattatcaattcttttttaa-tggacttgattagaaaaaatagctcactataatccttttaagtggtaataaatactcgaatcacaagattatttctttattttggggtttataaatctctaagtgccttatagataatatatttgagaaatttcttatatcgaactca........................................................... ................................................................cataacgtgagttcgatataagaaataaataaaaaatattcagtttcttcttgattataaacacattaagttattatcaattcttcttaaaatggacttgattacataaaacagaacactataatccttttaagtggtaataaatactcgaattagaagattatttctttattttagggtttataaatatctaagtgccttatagataatatattgaataagtttcttatatcgaactca........................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCCUUAGCGUUCCUUUUUCUCUUGUUACAACAAUGGCACAAUCAACAAAAUACGCAAUCGCAUAACGUGAGUUCGAUAUAAGAAUUAAAUGAAAAUAUUCCGUUUCUUGUGAUUAUAAGCAUAUUAAGUUAUUAUCAAUUCUUUUUUAAUGGACUUGAUUAGAAAAAAUAGCUCACUAUAAUCCUUUUAAGUGGUAAUAAAUACUCGAAUCACAAGAUUAUUUCUUUAUUUUGGGGUUUAUAAAUCUCUAAGUGCCUUAUAGAUAAUAUAUUUGAGAAAUUUCUUAUAUCGAACUCAGGUUCGCAUAAAUUAUUUACACGUAAAUAAAUAUUUCUUUACGUGUAGAGAAAUAUUUA ..........((((...........((((..((....))..))))..........))))....((..(((.(((((((((((((((((....................((((((((((...(((.((((...((...(((((.(((........))).)))))...))..)))))))((((.(((.....)))))))..............))))))))))..(((((((.....((..((((((((..(.......)..))))))))..)).....)))))))))))))))))))))))).))).))........((((((((((((.((....)).)))))))))))).......... (-79.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAUUUCUCUACACGUAAAGAAAUAUUUAUUUACGUGUAAAUAAUUUAUGCGAACCUGAGUUCGAUAUAAGAAAUUUCUCAAAUAUAUUAUCUAUAAGGCACUUAGAGAUUUAUAAACCCCAAAAUAAAGAAAUAAUCUUGUGAUUCGAGUAUUUAUUACCACUUAAAAGGAUUAUAGUGAGCUAUUUUUUCUAAUCAAGUCCAUUAAAAAAGAAUUGAUAAUAACUUAAUAUGCUUAUAAUCACAAGAAACGGAAUAUUUUCAUUUAAUUCUUAUAUCGAACUCACGUUAUGCGAUUGCGUAUUUUGUUGAUUGUGCCAUUGUUGUAACAAGAGAAAAAGGAACGCUAAGGAUUUA ............((((((((((..........)))))))))).........(((((((.(((((((((((((((((..........((((..((((.((((...)))).)))).))))....((.......(....)..((((((((((.(((((..(((((.........((((..((((....))))...)))).(((((.((..........)).))))).......))))))))))..))))))))))...))...............))))))))))))))))).))).))))...((((.((((.((..((((..((....))..))))..)).))))..)))).......... (-77.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 462 360 312 218 170 pint:PI0702|5end_conserved_hypothetical_protein;_possible_tetracenomycin_C_synthesis_protein_homolog_638640..638870_POSITIVE 432 360 311 139 90 pint:PI0619|5end_hypothetical_protein_569364..569594_POSITIVE 426 360 311 127 78 pint:PI0579|5end_hypothetical_protein_523419..523649_POSITIVE 426 355 317 211 173 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 426 355 317 197 159 pint:PI0111|5end_hypothetical_protein_108048..108278_POSITIVE 426 355 317 162 124 pint:PI0112|5end_hypothetical_protein_108013..108243_POSITIVE 400 359 314 141 96 pint:PI0983|5end_hypothetical_protein_909750..909980_POSITIVE 391 355 311 100 56 pint:PI1462|5end_hypothetical_protein_1385094..1385324_POSITIVE 368 348 319 159 130 pint:PI0130|5end_hypothetical_protein_122032..122262_POSITIVE 364 360 317 149 106 pint:PI1673|5end_hypothetical_protein_1587718..1587948_POSITIVE 362 330 284 224 176 pint:PI0172|5end_ISPg3-related_transposase_164262..164492_POSITIVE 360 360 317 131 84 pint:PI1450|5end_hypothetical_protein_1372683..1372913_POSITIVE 346 350 307 117 76 pint:PI0648|5end_hypothetical_protein_589448..589678_POSITIVE 318 350 306 230 185 pint:PI0599|5end_hypothetical_protein_547376..547606_POSITIVE 313 339 294 230 182 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 296 300 254 227 183 pint:PI0928|5end_hypothetical_protein_859851..860081_POSITIVE 295 348 306 210 166 pint:PI0173|5end_hypothetical_protein_165305..165535_POSITIVE 288 88 67 209 188 pint:PI1819|5end_hypothetical_protein_1756620..1756850_POSITIVE 287 348 301 219 173 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 282 88 62 32 7 pint:PI2071|5end_hypothetical_protein_2029908..2030138_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 385 360 311 61 12 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE 368 348 319 49 20 pint:PI0598|3end_hypothetical_protein_547233..547383_POSITIVE 346 360 313 90 43 pint:PI0725|3end_hypothetical_protein_658933..659083_POSITIVE 322 360 317 130 87 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 303 360 319 42 1 pint:PI2106|3end_hypothetical_protein_2059498..2059648_POSITIVE 295 348 306 63 19 pint:PI0172|3end_ISPg3-related_transposase_165238..165388_POSITIVE 294 109 63 106 56 pint:PI1714|3end_ISPg3-related_transposase_1631352..1631502_POSITIVE 294 86 53 85 52 pint:PI0326|3end_ISPg3-related_transposase_307768..307918_POSITIVE 281 360 314 57 11 pint:PI0533|3end_ABC_transporter,_permease_protein_488421..488571_POSITIVE 278 109 67 106 66 pint:PI1762|3end_ISPg3-related_transposase_1685645..1685795_POSITIVE 278 109 67 106 66 pint:PI1262|3end_ISPg3-related_transposase,_C-terminal_region_1184322..1184472_POSITIVE 278 109 67 106 66 pint:PI0298|3end_ISPg3-related_transposase_284664..284814_POSITIVE 277 88 68 136 116 pint:PI1019|3end_hypothetical_protein_938412..938562_POSITIVE 267 109 68 106 67 pint:PI2110|3end_ISPg3-related_transposase_(IS195_family)_2062446..2062596_POSITIVE 265 330 287 105 58 pint:PI1015|3end_conserved_hypothetical_protein_937347..937497_POSITIVE 265 350 320 41 11 pint:PI0808|3end_ISPg3-related_transposase_746457..746607_POSITIVE 262 80 34 149 88 pint:PI0202|3end_DNA_helicase_195189..195339_POSITIVE 261 326 284 63 21 pint:PI1260|3end_IS1001-related_transposase_1183272..1183422_POSITIVE 260 360 314 54 1 pint:PI0491|3end_hypothetical_protein_451227..451377_POSITIVE 259 360 330 35 5 pint:PI0701|3end_hypothetical_protein_638537..638687_POSITIVE