Origin IGS: taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctgtttaaaatcaattagatattaataattcaattcatttataactaaaaaattaaaattttatcattt .........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 aaatgataaaattttaattttttagttataaatgaattgaattattaatatctaattgattttaaacagattggatatttagctgccaaatgaatgccaacttttttccgcacattttcggcaaagataacaattaatagagaattacatttgaaattgacatcttttaactgttgctttttgcttgttttactacgttttctgcattattgcgacacttttataaattctttctgttctatatggtctattcataccttatgtgtttttaagttaaacatttggtattgaatacagatatactctgtgtttgtagttattataacttcgttgtttcataatagactgcttctcttgcctacaaatttacttatttagtatgatctaaacgaaaaaataaagacattatttcattttcaacctatgaaataatgtctttaatatatattaaggtgtattttctctataagcttggcacttta Mask Tandem Repeat Region ================================================ taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctgtttaaaatcaattagatattaataattcaattcatttataactaaaaaattaaaattttatcattt Find is-nt database================================================ Query_seq: PI1593:PI1594|PI1593:PI1594:3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II:MotA/TolQ/ExbB proton channel:->->:1523186..1523667 482 taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctgtttaaaatcaattagatattaataattcaattcatttataactaaaaaattaaaattttatcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1593:PI1594|PI1593:PI1594:3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II:MotA/TolQ/ExbB proton channel:->->:1523186..1523667 482 taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctgtttaaaatcaattagatattaataattcaattcatttataactaaaaaattaaaattttatcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1593:PI1594|PI1593:PI1594:3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II:MotA/TolQ/ExbB proton channel:->->:1523186..1523667 482 taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctgtttaaaatcaattagatattaataattcaattcatttataactaaaaaattaaaattttatcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctgtttaaaatcaattagatattaataattcaattcatttataactaaaaaattaaaattttatcattt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 117 End: 206 .................................................................................................................... M C R Q E K Q S I M K Q R S Y N N Y K H R V Y L Y S I P N V .................................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: - Start: 214 End: 312 ..................................................................................................................................................................................................................... F C M L Y S Y V M Y F L F F K Y F H R L L A S F T T F C A F L L M .......................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 195 End: 389 .................................................................................................................................................................................................. K F V C L T H I S W I S C F S N I F T D C Y H L F R L L V L L F C C N F S T L K L H L E R N I T I K A S F T R F F T P M ............................................................................................. taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctgtttaaaatcaattagatattaataattcaattcatttataactaaaaaattaaaattttatcattt 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================================================ taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctgtttaaaatcaattagatattaataattcaattcatttataactaaaaaattaaaattttatcattt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -9.0 Tail_Score: -3.10513 Start: 42 End: 86 Full_Region: gatctaaacgaaaaa ataaagacattatttcat tttcaacct atgaaataatgtctttaa tatatattaaggtgt .........................................ataaagacattatttcattttcaacctatgaaataatgtctttaa............................................................................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -12.5 Tail_Score: -5.38497 Start: 43 End: 85 Full_Region: CACCTTAATATATAT TAAAGACATTATTTCAT AGGTTGAAA ATGAAATAATGTCTTTA TTTTTTCGTTTAGAT ..........................................TAAAGACATTATTTCATAGGTTGAAAATGAAATAATGTCTTTA............................................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 83 HP_score: -8.9 Tail_Score: -3.93383 Start: 47 End: 81 Full_Region: aaacgaaaaaataaa gacattatttcat tttcaacct atgaaataatgtc tttaatatatattaa ..............................................gacattatttcattttcaacctatgaaataatgtc................................................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 54 HP_score: -3.0 Tail_Score: -4.15864 Start: 174 End: 190 Full_Region: acatttggtattgaa tacaga tatac tctgtg tttgtagttattata .............................................................................................................................................................................tacagatatactctgtg.................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 44 HP_score: -3.4 Tail_Score: -3.08798 Start: 176 End: 188 Full_Region: TAATAACTACAAACA CAGA GTATA TCTG TATTCAATACCAAAT ...............................................................................................................................................................................CAGAGTATATCTG...................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 50 HP_score: -3.4 Tail_Score: -3.65963 Start: 176 End: 188 Full_Region: atttggtattgaata caga tatac tctg tgtttgtagttatta ...............................................................................................................................................................................cagatatactctg...................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1593:PI1594|PI1593:PI1594:3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II:MotA/TolQ/ExbB proton channel:->->:1523186..1523667 482 taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctgtttaaaatcaattagatattaataattcaattcatttataactaaaaaattaaaattttatcattt Intra-Species Hit: Count: 1 Min: 1 Max: 416 Len: 416 Subject: pint_PI1593_PI1594|3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II:MotA/TolQ/ExbB proton channel|POSITIVE:POSITIVE|[1523186,1523667]|482 HSP 1 e-value: 0.0 bit: 825.0 Len: 416 Query Start:1 Query End:416 Subject Strand: POSITIVE Subject Start: 1 Subject End: 416 taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctg.................................................................. taaagtgccaagcttatagagaaaatacaccttaatatatattaaagacattatttcataggttgaaaatgaaataatgtctttattttttcgtttagatcatactaaataagtaaatttgtaggcaagagaagcagtctattatgaaacaacgaagttataataactacaaacacagagtatatctgtattcaataccaaatgtttaacttaaaaacacataaggtatgaatagaccatatagaacagaaagaatttataaaagtgtcgcaataatgcagaaaacgtagtaaaacaagcaaaaagcaacagttaaaagatgtcaatttcaaatgtaattctctattaattgttatctttgccgaaaatgtgcggaaaaaagttggcattcatttggcagctaaatatccaatctg.................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUGCCAAGCUUAUAGAGAAAAUACACCUUAAUAUAUAUUAAAGACAUUAUUUCAUAGGUUGAAAAUGAAAUAAUGUCUUUAUUUUUUCGUUUAGAUCAUACUAAAUAAGUAAAUUUGUAGGCAAGAGAAGCAGUCUAUUAUGAAACAACGAAGUUAUAAUAACUACAAACACAGAGUAUAUCUGUAUUCAAUACCAAAUGUUUAACUUAAAAACACAUAAGGUAUGAAUAGACCAUAUAGAACAGAAAGAAUUUAUAAAAGUGUCGCAAUAAUGCAGAAAACGUAGUAAAACAAGCAAAAAGCAACAGUUAAAAGAUGUCAAUUUCAAAUGUAAUUCUCUAUUAAUUGUUAUCUUUGCCGAAAAUGUGCGGAAAAAAGUUGGCAUUCAUUUGGCAGCUAAAUAUCCAAUCUG ...(((((((((...((((((((..((((.............(((((((((((((((((.........)))))))))))))))))...((((((.(((((..((((.....))))..((((....)))).......)))))..))))))....(((((((((...(((((..((((............((((((.((((..((((.............))))..)))))))))).....((((((..........))))))...)))).(((....))).......))))).......((.....)).............))).))))))...)))).))))))))....(((((.((((.(((........)))...)))).)))))....))))))).)).............. (-80.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGAUUGGAUAUUUAGCUGCCAAAUGAAUGCCAACUUUUUUCCGCACAUUUUCGGCAAAGAUAACAAUUAAUAGAGAAUUACAUUUGAAAUUGACAUCUUUUAACUGUUGCUUUUUGCUUGUUUUACUACGUUUUCUGCAUUAUUGCGACACUUUUAUAAAUUCUUUCUGUUCUAUAUGGUCUAUUCAUACCUUAUGUGUUUUUAAGUUAAACAUUUGGUAUUGAAUACAGAUAUACUCUGUGUUUGUAGUUAUUAUAACUUCGUUGUUUCAUAAUAGACUGCUUCUCUUGCCUACAAAUUUACUUAUUUAGUAUGAUCUAAACGAAAAAAUAAAGACAUUAUUUCAUUUUCAACCUAUGAAAUAAUGUCUUUAAUAUAUAUUAAGGUGUAUUUUCUCUAUAAGCUUGGCACUUUA ((..((((...........)))).))..((((((.(((((.(((........))).))))).........((((((((.(((...((((...(((..........((((((....(((.(((......)))......))).....))))))....(((((((.......))).))))..)))..)))).(((((((((((...(((((.........((((..(((((((((.....)))))))))((((((((((((((......)))..))))).))))))......)))).........)))))(((((......)))))........(((((((((((((((((.........)))))))))))))))))..))))).)))))))))..))))))))....))))))..... (-83.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 388 341 64 14 pint:PI1403|5end_conserved_hypothetical_protein_1323920..1324150_POSITIVE 294 401 361 193 163 pint:PI1038|5end_hypothetical_protein_958685..958915_POSITIVE 291 399 352 73 26 pint:PI1028|5end_glutamate_synthase,_small_subunit_943420..943650_POSITIVE 289 405 361 112 62 pint:PI1445|5end_hypothetical_protein_1368403..1368633_POSITIVE 273 400 359 77 42 pint:PI0175|5end_succinyl-CoA_synthetase_beta_subunit_167023..167253_POSITIVE 266 399 351 224 183 pint:PI2013|5end_hypothetical_protein_1972329..1972559_POSITIVE 263 391 351 181 137 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 258 407 361 52 15 pint:PI1680|5end_conserved_hypothetical_protein_1595038..1595268_POSITIVE 257 398 351 128 73 pint:PI1686|5end_hypothetical_protein_1601594..1601824_POSITIVE 257 409 362 211 169 pint:PI0937|5end_hypothetical_protein_869235..869465_POSITIVE 256 269 225 102 59 pint:PI1728|5end_ATP-dependent_Clp_protease,_proteolytic_subunit_1646916..1647146_POSITIVE 254 400 351 227 169 pint:PI1484|5end_conserved_hypothetical_protein_1404619..1404849_POSITIVE 252 400 351 207 170 pint:PI2080|5end_hypothetical_protein_2038093..2038323_POSITIVE 250 391 355 146 106 pint:PI0198|5end_hypothetical_protein_190719..190949_POSITIVE 250 410 361 118 73 pint:PI0168|5end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_161181..161411_POSITIVE 246 310 267 62 25 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 245 389 341 186 134 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 243 410 362 45 1 pint:PI0086|5end_possible_uroporphyrinogen-III_synthase_84944..85174_POSITIVE 241 395 354 93 37 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 239 33 1 222 186 pint:PI0998|5end_possible_flavin_reductase_domain_protein_922696..922926_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 85 43 48 6 pint:PI1593|3end_3,4-dihydroxy-2-butanone_4-phosphate_synthase/GTP_cyclohydrolase_II_1523125..1523275_POSITIVE 282 394 353 70 36 pint:PI1585|3end_ampG_permease_1514260..1514410_POSITIVE 280 375 342 121 84 pint:PI0572|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_517589..517739_POSITIVE 273 400 359 44 9 pint:PI0174|3end_succinyl-CoA_synthetase_alpha_subunit_167070..167220_POSITIVE 256 269 225 95 52 pint:PI1727|3end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1646989..1647139_POSITIVE 250 388 347 44 6 pint:PI1402|3end_3-deoxy-7-phosphoheptulonate_synthase_1323980..1324130_POSITIVE 250 410 361 115 70 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 248 157 124 79 42 pint:PI0399|3end_conserved_hypothetical_protein_364090..364240_POSITIVE 246 401 361 77 37 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 244 374 332 148 97 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE 243 402 361 125 67 pint:PI1097|3end_acetyltransferase,_GNAT_family_1021999..1022149_POSITIVE 237 400 359 97 55 pint:PI1149|3end_30S_ribosomal_protein_S18_1075757..1075907_POSITIVE 236 400 360 52 15 pint:PI0925|3end_ribosomal_protein_L11_methyltransferase_856638..856788_POSITIVE 234 289 242 59 11 pint:PI2151|3end_conserved_hypothetical_protein_2098252..2098402_POSITIVE 233 400 358 64 23 pint:PI2157|3end_xanthosine_triphosphate_pyrophosphatase,_HAM1_family_2104457..2104607_POSITIVE 229 387 341 85 44 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 229 130 81 102 58 pint:PI0726|3end_hypothetical_protein_659253..659403_POSITIVE 228 388 348 109 65 pint:PI0698|3end_conserved_hypothetical_protein_636711..636861_POSITIVE 226 160 112 113 51 pint:PI1284|3end_ATP_synthase,_delta_subunit_1200323..1200473_POSITIVE 225 387 348 50 1 pint:PI1069|3end_hypothetical_protein_988458..988608_POSITIVE