Origin IGS: tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagacaaaactaattgttactgattaaatttaggcggactctgcggagtccgcttttcttttttgcccttcccgtttatcttcagcacctgctttaaccacaaaaaggtaaattgctcactacataacgtgagttcgatataagaaataaataaaaaatattcagtttcttcttgattataaacacattaagttattatcaattcttcttaaaatggacttgattacataaaacagaacactataatccttttaagtggtaataaatactcgaattagaagattatttctttattttagggtttataaatatctaagtgccttatagataatatattgaataagtttcttatatcgaactcacgttactgtagtattcagcccctccccatgtgaggctacagaagccttcatacttattttttcaaacgaatttaataattatcaacattgctttcttctgaatatttcctttattaatattattcatgtagtttacttacacgcttcta Mask Tandem Repeat Region ================================================ tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta Find is-nt database================================================ Query_seq: PI0515:PI0516|PI0515:PI0516:conserved hypothetical protein:ferredoxin, 4Fe-4S:->->:475492..476003 512 tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0515:PI0516|PI0515:PI0516:conserved hypothetical protein:ferredoxin, 4Fe-4S:->->:475492..476003 512 tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0515:PI0516|PI0515:PI0516:conserved hypothetical protein:ferredoxin, 4Fe-4S:->->:475492..476003 512 tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 326 End: 415 ..................................................................................................................................................................................................................................................................................................................................... M F I I K K K L N I F Y L F L I S N S R Y V V S N L P F C G ................................................................................................. Protein_Len: 43 Strand: + Start: 364 End: 492 ........................................................................................................................................................................................................................................................................................................................................................................... M S Y I E L T L C S E Q F T F L W L K Q V L K I N G K G K K E K R T P Q S P P K F N Q .................... Protein_Len: 57 Strand: - Start: 2 End: 172 . S A H L Y V V H I I N I F S I N L L F C H Q Y N N F E N S F I L I F A E T A E C P S P S F V V T V H T R Y L F S M .................................................................................................................................................................................................................................................................................................................................................... tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta 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================================================ tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -10.1 Tail_Score: -2.68279 Start: 458 End: 479 Full_Region: AGGGCAAAAAAGAAA AGCGGACTC CGCA GAGTCCGCC TAAATTTAATCAGTA .........................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGCGGACTCCGCAGAGTCCGCC................................. Find igs database================================================ Query_seq: PI0515:PI0516|PI0515:PI0516:conserved hypothetical protein:ferredoxin, 4Fe-4S:->->:475492..476003 512 tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta Intra-Species Hit: Count: 2 Min: 1 Max: 512 Len: 512 Subject: pint_PI0515_PI0516|conserved hypothetical protein:ferredoxin, 4Fe-4S|POSITIVE:POSITIVE|[475492,476003]|512 HSP 1 e-value: 0.0 bit: 1015.0 Len: 512 Query Start:1 Query End:512 Subject Strand: POSITIVE Subject Start: 1 Subject End: 512 tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta tagaagcgtgtaagtaaactacatgaataatattaataaaggaaatattcagaagaaagcaatgttgataattattaaattcgtttgaaaaaataagtatgaaggcttctgtagcctcacatggggaggggctgaatactacagtaacgtgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatgtagtgagcaatttacctttttgtggttaaagcaggtgctgaagataaacgggaagggcaaaaaagaaaagcggactccgcagagtccgcctaaatttaatcagtaacaattagttttgtctta Subject: pint_PI0310_PI0312|outer membrane protein:hypothetical protein|POSITIVE:POSITIVE|[294371,294730]|360 HSP 1 e-value: 1.0E-68 bit: 262.0 Len: 240 Query Start:150 Query End:389 Subject Strand: NEGATIVE Subject Start: 65 Subject End: 301 .....................................................................................................................................................tgagttcgatataagaaacttattcaatatattatctataaggcacttagatatttataaaccctaaaataaagaaataatcttctaattcgagtatttattaccacttaaaaggattatagtgttctgttttatgtaatcaagtccattttaagaagaattgataataacttaatgtgtttataatcaagaagaaactgaatattttttatttatttcttatatcgaactcacgttatg........................................................................................................................... .....................................................................................................................................................tgagttcgatataagaaatttctcaaatatattatctataaggcacttagagatttataaaccccaaaataaagaaataatcttgtgattcgagtatttattaccacttaaaaggattatagtgagctattttttctaatcaagtcca-ttaaaaaagaattgataataacttaatatgcttataatc-acaagaaacggaata-ttttcatttaattcttatatcgaactcacgttatg........................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAGCGUGUAAGUAAACUACAUGAAUAAUAUUAAUAAAGGAAAUAUUCAGAAGAAAGCAAUGUUGAUAAUUAUUAAAUUCGUUUGAAAAAAUAAGUAUGAAGGCUUCUGUAGCCUCACAUGGGGAGGGGCUGAAUACUACAGUAACGUGAGUUCGAUAUAAGAAACUUAUUCAAUAUAUUAUCUAUAAGGCACUUAGAUAUUUAUAAACCCUAAAAUAAAGAAAUAAUCUUCUAAUUCGAGUAUUUAUUACCACUUAAAAGGAUUAUAGUGUUCUGUUUUAUGUAAUCAAGUCCAUUUUAAGAAGAAUUGAUAAUAACUUAAUGUGUUUAUAAUCAAGAAGAAACUGAAUAUUUUUUAUUUAUUUCUUAUAUCGAACUCACGUUAUGUAGUGAGCAAUUUACCUUUUUGUGGUUAAAGCAGGUGCUGAAGAUAAACGGGAAGGGCAAAAAAGAAAAGCGGACUCCGCAGAGUCCGCCUAAAUUUAAUCAGUAACAAUUAGUUUUGUCUUA ......((((((.......)))))).......(((((((....(((((((........).)))))).....)))))))..(((((((........(((((..(((((.....)))))..(((..(((((.(((...(((((((.(((((((((((((((((((((((.........((((.((((((.........))))))..)))).......((((((((((....(((((((((((..(((.....)))..((((((((((((((((....))))............))))).)))))))..)))))(((.(((((.......).)))).))).)))))).........)))))))))).)))))))))))))))))))))))))))))))))......)))))..)))..........))))).....)))))))..(((((((((.......((((((((....)))))))).......((((........)))).))))))))). (-121.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGACAAAACUAAUUGUUACUGAUUAAAUUUAGGCGGACUCUGCGGAGUCCGCUUUUCUUUUUUGCCCUUCCCGUUUAUCUUCAGCACCUGCUUUAACCACAAAAAGGUAAAUUGCUCACUACAUAACGUGAGUUCGAUAUAAGAAAUAAAUAAAAAAUAUUCAGUUUCUUCUUGAUUAUAAACACAUUAAGUUAUUAUCAAUUCUUCUUAAAAUGGACUUGAUUACAUAAAACAGAACACUAUAAUCCUUUUAAGUGGUAAUAAAUACUCGAAUUAGAAGAUUAUUUCUUUAUUUUAGGGUUUAUAAAUAUCUAAGUGCCUUAUAGAUAAUAUAUUGAAUAAGUUUCUUAUAUCGAACUCACGUUACUGUAGUAUUCAGCCCCUCCCCAUGUGAGGCUACAGAAGCCUUCAUACUUAUUUUUUCAAACGAAUUUAAUAAUUAUCAACAUUGCUUUCUUCUGAAUAUUUCCUUUAUUAAUAUUAUUCAUGUAGUUUACUUACACGCUUCUA ...(((((......))))).............((((((((((....)))))))))).........((.................(((....)))............(((((((((((..((((((((((((((((((((((((((((((..........((((((((.((((((.(((((((...........((((.(((((.(((.........))).)))))...))))..........)))))))..((..((((........))))..))..))))))........((((((((((((................)))))).))))))...)))))))).)))))))))))))))))))))))).))))))((((((..........(((((((((.....)))).))))).(((((..(((....)))...)))))...................))))))........................)))))))))))....))..... (-113.69) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 602 230 181 231 182 pint:PI0312|5end_hypothetical_protein_294591..294821_POSITIVE 403 404 365 211 176 pint:PI0172|5end_ISPg3-related_transposase_164262..164492_POSITIVE 375 460 413 95 52 pint:PI0628|5end_phosphoribosylglycinamide_formyltransferase_576027..576257_POSITIVE 339 399 365 214 176 pint:PI0326|5end_ISPg3-related_transposase_306792..307022_POSITIVE 330 392 365 204 176 pint:PI1762|5end_ISPg3-related_transposase_1684669..1684899_POSITIVE 317 177 137 135 96 pint:PI0299|5end_hypothetical_protein_284623..284853_POSITIVE 316 169 121 179 119 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 316 156 119 128 101 pint:PI0164|5end_conserved_hypothetical_protein_158478..158708_POSITIVE 311 404 365 210 176 pint:PI1261|5end_ISPg3-related_transposase,_N-terminal_region_1183347..1183577_POSITIVE 306 163 133 231 191 pint:PI0173|5end_hypothetical_protein_165305..165535_POSITIVE 305 149 102 227 167 pint:PI0404|5end_integrase_371295..371525_POSITIVE 301 396 365 201 176 pint:PI2110|5end_ISPg3-related_transposase_(IS195_family)_2061470..2061700_POSITIVE 300 410 365 220 176 pint:PI1714|5end_ISPg3-related_transposase_1630376..1630606_POSITIVE 300 132 93 132 93 pint:PI0574|5end_hypothetical_protein_519260..519490_POSITIVE 300 160 114 71 23 pint:PI0256|5end_conjugative_transposon_protein,_TraE_249044..249274_POSITIVE 298 480 439 159 118 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 298 480 439 83 42 pint:PI0669|5end_hypothetical_protein_610924..611154_POSITIVE 297 167 145 210 188 pint:PI1819|5end_hypothetical_protein_1756620..1756850_POSITIVE 297 387 365 198 176 pint:PI0808|5end_ISPg3-related_transposase_745481..745711_POSITIVE 296 159 116 110 71 pint:PI2053|5end_conserved_hypothetical_protein;_possible_outer_membrane_receptor_protein_2010673..2010903_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 405 156 120 146 108 pint:PI0059|3end_peptide_chain_release_factor_RF-2_58171..58321_POSITIVE 375 460 413 69 26 pint:PI0627|3end_conserved_hypothetical_protein_576081..576231_POSITIVE 369 397 355 99 58 pint:PI1934|3end_hypothetical_protein_1882601..1882751_POSITIVE 349 177 133 96 44 pint:PI0172|3end_ISPg3-related_transposase_165238..165388_POSITIVE 343 164 122 85 50 pint:PI2110|3end_ISPg3-related_transposase_(IS195_family)_2062446..2062596_POSITIVE 343 397 366 33 3 pint:PI0310|3end_outer_membrane_protein_294310..294460_POSITIVE 339 399 365 86 48 pint:PI0325|3end_ISPg3-related_transposase_fragment_306744..306894_POSITIVE 330 392 365 112 84 pint:PI1760|3end_hypothetical_protein_1684657..1684807_POSITIVE 317 177 137 96 57 pint:PI0298|3end_ISPg3-related_transposase_284664..284814_POSITIVE 312 177 133 96 53 pint:PI0808|3end_ISPg3-related_transposase_746457..746607_POSITIVE 311 404 365 55 21 pint:PI1260|3end_IS1001-related_transposase_1183272..1183422_POSITIVE 309 186 144 102 65 pint:PI1762|3end_ISPg3-related_transposase_1685645..1685795_POSITIVE 308 480 438 52 5 pint:PI1828|3end_peptidase,_M23/M37_family,_C-terminal_1769089..1769239_POSITIVE 302 164 121 85 46 pint:PI0326|3end_ISPg3-related_transposase_307768..307918_POSITIVE 300 454 411 54 4 pint:PI0953|3end_hypothetical_protein_885390..885540_POSITIVE 300 454 411 112 62 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 300 139 96 141 95 pint:PI0242|3end_hypothetical_protein_240227..240377_POSITIVE 296 470 422 102 47 pint:PI0008|3end_exoribonuclease_II_(ribonuclease_II)_9561..9711_POSITIVE 292 406 368 94 58 pint:PI1015|3end_conserved_hypothetical_protein_937347..937497_POSITIVE 291 405 368 121 87 pint:PI0710|3end_hypothetical_protein_648004..648154_POSITIVE