Origin IGS: ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca .........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 tgatgcgcactgcaacgacacagaatcacgcactgggagaagcgcattatacacgccgacacgataatacgggaaagagacagacattagtctttttcaaatatgacgtcatattcgcgcaaatatgacgtcatatttggcagaaaatgacgtcatatttttctgagcatctaccttgcaagatgtttttaaggtttatactataataagtaatgtgtaaatacttgctattctgccaacaaatacgtacctttgcacgctgaaaaaacaagaaggaaagttaatgaaaaaactctatatagagacatatggctgccag Mask Tandem Repeat Region ================================================ ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca Find is-nt database================================================ Query_seq: PI0107:PI0108|PI0107:PI0108:2-methylthioadenine synthetase:L-lactate permease:->->:104713..105031 319 ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0107:PI0108|PI0107:PI0108:2-methylthioadenine synthetase:L-lactate permease:->->:104713..105031 319 ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0107:PI0108|PI0107:PI0108:2-methylthioadenine synthetase:L-lactate permease:->->:104713..105031 319 ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 49 End: 186 ................................................ M F F Q R A K V R I C W Q N S K Y L H I T Y Y S I N L K N I L Q G R C S E K Y D V I F C Q I ..................................................................................................................................... Protein_Len: 41 Strand: - Start: 195 End: 317 .................................................................................................................................................................................................. I Q A F I V D Y K F F V L T Q R K G T N D H R R T Y H A E G L A H N Q T T A T R M .. Protein_Len: 33 Strand: - Start: 1 End: 99 Q C G Y T E I Y L K K M L K G E Q K K L T C L Y T N T P L I A L M ............................................................................................................................................................................................................................ ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca 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================================================ ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -9.8 Tail_Score: -3.55071 Start: 163 End: 196 Full_Region: AGATGCTCAGAAAAA TATGACGTCATTTT CTGCCA AATATGACGTCATA TTTGCGCGAATATGA ..................................................................................................................................................................TATGACGTCATTTTCTGCCAAATATGACGTCATA........................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -16.7 Tail_Score: -3.53444 Start: 163 End: 218 Full_Region: AGATGCTCAGAAAAA TATGACGTCATTTTCTGCCAAATATG ACGT CATATTTGCGCGAATATGACGTCATA TTTGAAAAAGACTAA ..................................................................................................................................................................TATGACGTCATTTTCTGCCAAATATGACGTCATATTTGCGCGAATATGACGTCATA..................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -16.7 Tail_Score: -4.84761 Start: 163 End: 218 Full_Region: ttagtctttttcaaa tatgacgtcatattcgcgcaaatatg acgt catatttggcagaaaatgacgtcata tttttctgagcatct ..................................................................................................................................................................tatgacgtcatattcgcgcaaatatgacgtcatatttggcagaaaatgacgtcata..................................................................................................... Find igs database================================================ Query_seq: PI0107:PI0108|PI0107:PI0108:2-methylthioadenine synthetase:L-lactate permease:->->:104713..105031 319 ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca Intra-Species Hit: Count: 1 Min: 1 Max: 319 Len: 319 Subject: pint_PI0107_PI0108|2-methylthioadenine synthetase:L-lactate permease|POSITIVE:POSITIVE|[104713,105031]|319 HSP 1 e-value: 1.0E-180 bit: 632.0 Len: 319 Query Start:1 Query End:319 Subject Strand: POSITIVE Subject Start: 1 Subject End: 319 ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca ctggcagccatatgtctctatatagagttttttcattaactttccttcttgttttttcagcgtgcaaaggtacgtatttgttggcagaatagcaagtatttacacattacttattatagtataaaccttaaaaacatcttgcaaggtagatgctcagaaaaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatatttgaaaaagactaatgtctgtctctttcccgtattatcgtgtcggcgtgtataatgcgcttctcccagtgcgtgattctgtgtcgttgcagtgcgcatca HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 42 Query Start:181 Query End:222 Subject Strand: NEGATIVE Subject Start: 181 Subject End: 222 ....................................................................................................................................................................................caaatatgacgtcatatttgcgcgaatatgacgtcatatttg................................................................................................. ....................................................................................................................................................................................caaatatgacgtcatattcgcgcaaatatgacgtcatatttg................................................................................................. HSP 3 e-value: 5.0E-8 bit: 60.0 Len: 62 Query Start:160 Query End:221 Subject Strand: NEGATIVE Subject Start: 160 Subject End: 221 ...............................................................................................................................................................aaatatgacgtcattttctgccaaatatgacgtcatatttgcgcgaatatgacgtcatattt.................................................................................................. ...............................................................................................................................................................aaatatgacgtcatattcgcgcaaatatgacgtcatatttggcagaaaatgacgtcatattt.................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGGCAGCCAUAUGUCUCUAUAUAGAGUUUUUUCAUUAACUUUCCUUCUUGUUUUUUCAGCGUGCAAAGGUACGUAUUUGUUGGCAGAAUAGCAAGUAUUUACACAUUACUUAUUAUAGUAUAAACCUUAAAAACAUCUUGCAAGGUAGAUGCUCAGAAAAAUAUGACGUCAUUUUCUGCCAAAUAUGACGUCAUAUUUGCGCGAAUAUGACGUCAUAUUUGAAAAAGACUAAUGUCUGUCUCUUUCCCGUAUUAUCGUGUCGGCGUGUAUAAUGCGCUUCUCCCAGUGCGUGAUUCUGUGUCGUUGCAGUGCGCAUCA ..(((((.(((..((((.......(((......((((.(((((.(....(((((((..((.((......(((.((((((((((......)))))))))).)))....((((......))))...)))).)))))))....).))))).)))))))....((((((((((((((.(((.((((((((((....)))))))).))))).)))))))))))))).....))))..))).))))).......((((((((((((....)))).)))))))).........((((((....((((......)))).)))))).. (-86.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGCGCACUGCAACGACACAGAAUCACGCACUGGGAGAAGCGCAUUAUACACGCCGACACGAUAAUACGGGAAAGAGACAGACAUUAGUCUUUUUCAAAUAUGACGUCAUAUUCGCGCAAAUAUGACGUCAUAUUUGGCAGAAAAUGACGUCAUAUUUUUCUGAGCAUCUACCUUGCAAGAUGUUUUUAAGGUUUAUACUAUAAUAAGUAAUGUGUAAAUACUUGCUAUUCUGCCAACAAAUACGUACCUUUGCACGCUGAAAAAACAAGAAGGAAAGUUAAUGAAAAAACUCUAUAUAGAGACAUAUGGCUGCCAG ((((((((.(((........)))..(((.....))).....)))))))).....((((.........((((.(((((((((........))))))))).((((((((((((((((......))))))))))))))))((((((((...................((((((((........)))))))).((((((((((((.............)))))))).))))...)))))))).......))))(((((......(....).....)))))................((((....)))).....))))...... (-79.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 654 210 161 153 104 pint:PI0063|5end_transcriptional_regulator,_GntR_family_63181..63411_POSITIVE 525 230 183 202 151 pint:PI0163|5end_conserved_hypothetical_protein_157116..157346_POSITIVE 392 307 262 224 189 pint:PI1877|5end_hypothetical_protein_1819910..1820140_POSITIVE 387 289 248 52 1 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 378 309 262 224 177 pint:PI0896|5end_2-oxoglutarate_oxidoreductase,_alpha_subunit_827138..827368_POSITIVE 351 300 257 49 10 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 341 308 262 135 83 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 332 306 261 211 167 pint:PI0251|5end_hypothetical_protein_247551..247781_POSITIVE 327 308 263 167 120 pint:PI1864|5end_chromate_transport_protein_1810318..1810548_POSITIVE 322 103 62 162 115 pint:PI0228|5end_outer_membrane_cobalamin_receptor_protein_225752..225982_POSITIVE 318 279 234 176 128 pint:PI0733|5end_membrane_protein;_predicted_exporter_664389..664619_POSITIVE 316 200 155 184 139 pint:PI0001|5end_possible_Ton-B_receptor_400..630_POSITIVE 315 310 262 163 108 pint:PI1166|5end_hypothetical_protein_1089305..1089535_POSITIVE 306 308 264 83 26 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 305 310 261 171 129 pint:PI1285|5end_ATP_synthase,_B_subunit_1200348..1200578_POSITIVE 303 310 263 101 55 pint:PI1875|5end_hypothetical_protein_1818934..1819164_POSITIVE 302 93 51 231 187 pint:PI2003|5end_hypothetical_protein_1960823..1961053_POSITIVE 302 93 51 70 26 pint:PI2002|5end_hypothetical_protein_1960662..1960892_POSITIVE 302 93 51 97 53 pint:PI1604|5end_hypothetical_protein_1534017..1534247_POSITIVE 302 93 51 58 14 pint:PI1129|5end_hypothetical_protein_1055377..1055607_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 300 256 64 21 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 345 295 252 132 83 pint:PI0780|3end_DNA_gyrase,_subunit_A_(DNA_topoisomerase_(ATP-hydrolyzing))_718513..718663_POSITIVE 322 93 60 130 93 pint:PI0592|3end_DNA_mismatch_repair_protein_542611..542761_POSITIVE 318 279 234 74 26 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 306 308 264 135 78 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 306 276 231 143 88 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 305 310 261 66 24 pint:PI1284|3end_ATP_synthase,_delta_subunit_1200323..1200473_POSITIVE 302 93 51 53 9 pint:PI0996|3end_hypothetical_protein_920660..920810_POSITIVE 302 93 51 112 68 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 300 269 230 53 7 pint:PI0758|3end_hypothetical_protein_690506..690656_POSITIVE 299 300 256 59 13 pint:PI1505|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_1425409..1425559_POSITIVE 294 290 242 143 107 pint:PI0090|3end_amidophosphoribosyltransferase_89160..89310_POSITIVE 293 306 262 141 94 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 292 309 261 82 40 pint:PI2125|3end_D-tyrosyl-tRNA(Tyr)_deacylase_2074979..2075129_POSITIVE 288 305 262 56 5 pint:PI2044|3end_hypothetical_protein_1997351..1997501_POSITIVE 288 270 228 149 109 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 288 309 263 66 8 pint:PI0747|3end_possible_mobilization_protein_676702..676852_POSITIVE 285 308 262 76 28 pint:PI0017|3end_thiol-disulfide_isomerase;_thioredoxin_22835..22985_POSITIVE 284 308 263 50 6 pint:PI1145|3end_50S_ribosomal_protein_L35_1072794..1072944_POSITIVE 284 279 232 149 112 pint:PI0036|3end_glutathione_peroxidase_39289..39439_POSITIVE