Origin IGS: tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta .........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 taaaatcaatataagctattccaccgtcattctatatatcttttttatacgcacggagaggataaaaacaaacaataacacctctctttcaatattaatataaaataatgcgaaaattcacaattaaataatcttatattttgattttccccaattattcattatatttgcaaatagaataaatacatattattaatctaagttttatgaacaacaacaaagttatgaaccgcgcggcggacaatatcagaattctcgctgcttccatggtggagaaagcaaaatcaggacaccctggaggagca Mask Tandem Repeat Region ================================================ tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta Find is-nt database================================================ Query_seq: PI0891:PI0892|PI0891:PI0892:transketolase:acyl-ACP thioesterase:->->:822966..823270 305 tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0891:PI0892|PI0891:PI0892:transketolase:acyl-ACP thioesterase:->->:822966..823270 305 tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0891:PI0892|PI0891:PI0892:transketolase:acyl-ACP thioesterase:->->:822966..823270 305 tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 38 End: 148 ..................................... M E A A R I L I L S A A R F I T L L L F I K L R L I I C I Y S I C K Y N E ............................................................................................................................................................. Protein_Len: 37 Strand: + Start: 148 End: 258 ................................................................................................................................................... M I G E N Q N I R L F N C E F S H Y F I L I L K E R C Y C L F L S S P C V ............................................... Protein_Len: 33 Strand: + Start: 189 End: 287 ............................................................................................................................................................................................ M F A L F Y I N I E R E V L L F V F I L S V R I K K I Y R M T V E .................. Protein_Len: 32 Strand: - Start: 206 End: 301 ............................................................................................................................................................................................................. I L I S L S T N N N T K I R E T R I F F I Y L I V T S Y S I N M .... Protein_Len: 41 Strand: - Start: 1 End: 123 A G G P H G S K A K E V M S A A L I R I N D A A R N M V K N N N M F S L N I I H M ...................................................................................................................................................................................... tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta 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================================================ tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -8.2 Tail_Score: -3.27617 Start: 66 End: 76 Full_Region: GAATTCTGATATTGT CCGC CGC GCGG TTCATAACTTTGTTG .................................................................CCGCCGCGCGG..................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0891:PI0892|PI0891:PI0892:transketolase:acyl-ACP thioesterase:->->:822966..823270 305 tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta Intra-Species Hit: Count: 1 Min: 1 Max: 305 Len: 305 Subject: pint_PI0891_PI0892|transketolase:acyl-ACP thioesterase|POSITIVE:POSITIVE|[822966,823270]|305 HSP 1 e-value: 1.0E-172 bit: 605.0 Len: 305 Query Start:1 Query End:305 Subject Strand: POSITIVE Subject Start: 1 Subject End: 305 tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta tgctcctccagggtgtcctgattttgctttctccaccatggaagcagcgagaattctgatattgtccgccgcgcggttcataactttgttgttgttcataaaacttagattaataatatgtatttattctatttgcaaatataatgaataattggggaaaatcaaaatataagattatttaattgtgaattttcgcattattttatattaatattgaaagagaggtgttattgtttgtttttatcctctccgtgcgtataaaaaagatatatagaatgacggtggaatagcttatattgatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUCCUCCAGGGUGUCCUGAUUUUGCUUUCUCCACCAUGGAAGCAGCGAGAAUUCUGAUAUUGUCCGCCGCGCGGUUCAUAACUUUGUUGUUGUUCAUAAAACUUAGAUUAAUAAUAUGUAUUUAUUCUAUUUGCAAAUAUAAUGAAUAAUUGGGGAAAAUCAAAAUAUAAGAUUAUUUAAUUGUGAAUUUUCGCAUUAUUUUAUAUUAAUAUUGAAAGAGAGGUGUUAUUGUUUGUUUUUAUCCUCUCCGUGCGUAUAAAAAAGAUAUAUAGAAUGACGGUGGAAUAGCUUAUAUUGAUUUUA ........((((....)))).....(((...((((((.(((((((((((((.....(((......((((...)))).)))....))))))))).))))..................(((((((((.((.(((.((((((((((..(((((((.(.(((((.((((((((......))))).....))).))))).))))))))))))))..........((((((...................))))))..)))).))).)).))))))))).......))))))..))).............. (-60.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUCAAUAUAAGCUAUUCCACCGUCAUUCUAUAUAUCUUUUUUAUACGCACGGAGAGGAUAAAAACAAACAAUAACACCUCUCUUUCAAUAUUAAUAUAAAAUAAUGCGAAAAUUCACAAUUAAAUAAUCUUAUAUUUUGAUUUUCCCCAAUUAUUCAUUAUAUUUGCAAAUAGAAUAAAUACAUAUUAUUAAUCUAAGUUUUAUGAACAACAACAAAGUUAUGAACCGCGCGGCGGACAAUAUCAGAAUUCUCGCUGCUUCCAUGGUGGAGAAAGCAAAAUCAGGACACCCUGGAGGAGCA ..............(((.(((((((((.......((((.......)))).((..(((((((...................)))))))......................((((.(((((..............((((((((((...........((((((................))))))...((((..(((......)))..))))........))))).))))).((((...)))).........))))).)))).))....))))))))).........(((((....)))))...))). (-53.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 77 33 180 119 pint:PI1849|5end_conserved_hypothetical_protein;_possible_acyltransferase_family_protein_1794916..1795146_POSITIVE 348 88 44 79 20 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 344 80 39 53 6 pint:PI1865|5end_chromate_transport_protein_1810935..1811165_POSITIVE 335 77 31 145 101 pint:PI1632|5end_hypothetical_protein_1552819..1553049_POSITIVE 329 89 44 185 122 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 329 89 44 82 19 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 327 78 35 151 108 pint:PI1879|5end_uracil_phosphoribosyltransferase_1820671..1820901_POSITIVE 326 97 56 163 125 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 322 49 1 158 112 pint:PI1847|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_1792006..1792236_POSITIVE 322 73 31 162 101 pint:PI0339|5end_hypothetical_protein_315735..315965_POSITIVE 320 57 12 60 5 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 319 78 31 117 70 pint:PI0707|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_643358..643588_POSITIVE 316 77 32 225 173 pint:PI2135|5end_conserved_hypothetical_protein_2082754..2082984_POSITIVE 316 77 32 76 24 pint:PI2136|5end_hypothetical_protein_2082605..2082835_POSITIVE 316 50 6 192 144 pint:PI1322|5end_nucleoside_permease_1240324..1240554_POSITIVE 316 71 31 125 68 pint:PI1009|5end_cytochrome_c_nitrite_reductase,_large_subunit_929342..929572_POSITIVE 313 77 32 73 37 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 312 100 53 92 36 pint:PI0706|5end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_642226..642456_POSITIVE 309 47 1 76 19 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 308 87 44 148 100 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 50 1 134 70 pint:PI1575|3end_LemA_protein_1501852..1502002_POSITIVE 328 78 32 117 62 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 327 80 40 47 1 pint:PI1864|3end_chromate_transport_protein_1811009..1811159_POSITIVE 325 89 44 60 1 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE 320 57 12 60 5 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 319 78 31 73 26 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 313 77 32 64 28 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 312 100 53 57 1 pint:PI0705|3end_conserved_hypothetical_protein;_possible_lipoprotein_642271..642421_POSITIVE 309 47 1 76 19 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 304 75 33 148 110 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 303 88 41 54 14 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 296 77 43 138 102 pint:PI0415|3end_malate_dehydrogenase_386427..386577_POSITIVE 290 77 33 43 1 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 288 47 5 70 27 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 287 51 11 135 93 pint:PI0582|3end_hypothetical_protein_525214..525364_POSITIVE 287 76 33 143 103 pint:PI0120|3end_glutamate_racemase_112697..112847_POSITIVE 283 90 47 92 47 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 282 106 66 135 101 pint:PI1423|3end_hypothetical_protein_1343011..1343161_POSITIVE 282 48 1 132 77 pint:PI0140|3end_conserved_hypothetical_protein_132106..132256_POSITIVE 277 73 33 60 1 pint:PI0338|3end_hypothetical_protein_315713..315863_POSITIVE