Origin IGS: ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgactttcaaagcaaaaacagcaaataaaaaaggagcaaagcaaccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta .........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 taaataagatatagtcagcatacacttgtaaagctgaaaaggagcgaagcaacgaataatggttgctttgctccttttttatttgctgtttttgctttgaaagtcagtattattattctttgtctatggtatgataattaattatcataccgatgttaatcaattatcataccgatgataatgcattatcatattgatgacaatcaattatcatactgatgataaagtattattatacagataaaccgaaaaaactttcagcttcttttgctattcttgaggtacaacgttctgctaaaatcctaaattttaggtattgtgtgagtaagtgaatgatggtacctttgcattctaaaaaacatattatcaataaaaggctgaacactaagagaaggttcacaatactttagtataagaaattaacaattaaaagaacaaaa Mask Tandem Repeat Region ================================================ ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaccatagacaaagaataataatactgactttcaaagcaaaaacagcaaataaaaaaggagcaaagcaaccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta Find is-nt database================================================ Query_seq: PI1675:PI1676|PI1675:PI1676:TonB-dependent outer membrane receptor:phosphatidate cytidylyltransferase:->->:1590596..1591035 440 ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgactttcaaagcaaaaacagcaaataaaaaaggagcaaagcaaccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1675:PI1676|PI1675:PI1676:TonB-dependent outer membrane receptor:phosphatidate cytidylyltransferase:->->:1590596..1591035 440 ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgactttcaaagcaaaaacagcaaataaaaaaggagcaaagcaaccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1675:PI1676|PI1675:PI1676:TonB-dependent outer membrane receptor:phosphatidate cytidylyltransferase:->->:1590596..1591035 440 ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgactttcaaagcaaaaacagcaaataaaaaaggagcaaagcaaccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgactttcaaagcaaaaacagcaaataaaaaaggagcaaagcaaccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 28 End: 135 ........................... M L K Y C E P S L S V Q P F I D N M F F R M Q R Y H H S L T H T I P K I ................................................................................................................................................................................................................................................................................................................. Protein_Len: 56 Strand: + Start: 38 End: 205 ..................................... M V N L L L V F S L L L I I C F L E C K G T I I H L L T Q Y L K F R I L A E R C T S R I A K E A E S F F G L S V ........................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 325 End: 423 .................................................................................................................................................................................................................................................................................................................................... M I I L T F K A K T A N K K G A K Q P L F V A S L L F S F T S V C ................. Protein_Len: 45 Strand: - Start: 303 End: 437 .............................................................................................................................................................................................................................................................................................................. N D Y W L C L I I I S V K L A F V A F L F P A F C G N N T A E S R K L K V L T H Q S Y R M ... Protein_Len: 41 Strand: - Start: 112 End: 234 ............................................................................................................... K S V C Y R F N L I K A S R Q V E L I A F S A S L K K P K D T Y Y Y K I M L I I M .............................................................................................................................................................................................................. ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgactttcaaagcaaaaacagcaaataaaaaaggagcaaagcaaccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta 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: 86 Start: 237 End: 266 ............................................................................................................................................................................................................................................ATTGTCATCAATATGATAATGCATTATCAT.............................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 227 End: 256 ..................................................................................................................................................................................................................................ATTATCATATTGATGACAATCAATTATCAT........................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 281 End: 310 ........................................................................................................................................................................................................................................................................................ATTAACATCGGTATGATAATTAATTATCAT.................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 293 End: 322 ....................................................................................................................................................................................................................................................................................................TTTGTCTATGGTATGATAATTAATTATCAT...................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 249 End: 278 ........................................................................................................................................................................................................................................................ATTATCATACCGATGATAATGCATTATCAT.................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgactttcaaagcaaaaacagcaaataaaaaaggagcaaagcaaccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 50 HP_score: -4.7 Tail_Score: -2.59793 Start: 128 End: 146 Full_Region: aggtacaacgttctg ctaaaat cctaa attttag gtattgtgtgagtaa ...............................................................................................................................ctaaaatcctaaattttag...................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 78 HP_score: -9.9 Tail_Score: -2.50338 Start: 289 End: 314 Full_Region: attattctttgtcta tggtatgataa ttaa ttatcataccg atgttaatcaattat ................................................................................................................................................................................................................................................................................................tggtatgataattaattatcataccg.............................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -14.7 Tail_Score: -5.69793 Start: 367 End: 400 Full_Region: ttgtaaagctgaaaa ggagcgaagcaacga ataa tggttgctttgctcc ttttttatttgctgt ..............................................................................................................................................................................................................................................................................................................................................................................ggagcgaagcaacgaataatggttgctttgctcc........................................ Find igs database================================================ Query_seq: PI1675:PI1676|PI1675:PI1676:TonB-dependent outer membrane receptor:phosphatidate cytidylyltransferase:->->:1590596..1591035 440 ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgactttcaaagcaaaaacagcaaataaaaaaggagcaaagcaaccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta Intra-Species Hit: Count: 1 Min: 1 Max: 440 Len: 440 Subject: pint_PI1675_PI1676|TonB-dependent outer membrane receptor:phosphatidate cytidylyltransferase|POSITIVE:POSITIVE|[1590596, 1591035]|440 HSP 1 e-value: 0.0 bit: 676.0 Len: 341 Query Start:1 Query End:341 Subject Strand: POSITIVE Subject Start: 1 Subject End: 341 ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgacttt................................................................................................... ttttgttcttttaattgttaatttcttatactaaagtattgtgaaccttctcttagtgttcagccttttattgataatatgttttttagaatgcaaaggtaccatcattcacttactcacacaatacctaaaatttaggattttagcagaacgttgtacctcaagaatagcaaaagaagctgaaagttttttcggtttatctgtataataatactttatcatcagtatgataattgattgtcatcaatatgataatgcattatcatcggtatgataattgattaacatcggtatgataattaattatcataccatagacaaagaataataatactgacttt................................................................................................... HSP 2 e-value: 6.0E-27 bit: 123.0 Len: 62 Query Start:379 Query End:440 Subject Strand: POSITIVE Subject Start: 379 Subject End: 440 ..........................................................................................................................................................................................................................................................................................................................................................................................ccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta ..........................................................................................................................................................................................................................................................................................................................................................................................ccattattcgttgcttcgctccttttcagctttacaagtgtatgctgactatatcttattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGUUCUUUUAAUUGUUAAUUUCUUAUACUAAAGUAUUGUGAACCUUCUCUUAGUGUUCAGCCUUUUAUUGAUAAUAUGUUUUUUAGAAUGCAAAGGUACCAUCAUUCACUUACUCACACAAUACCUAAAAUUUAGGAUUUUAGCAGAACGUUGUACCUCAAGAAUAGCAAAAGAAGCUGAAAGUUUUUUCGGUUUAUCUGUAUAAUAAUACUUUAUCAUCAGUAUGAUAAUUGAUUGUCAUCAAUAUGAUAAUGCAUUAUCAUCGGUAUGAUAAUUGAUUAACAUCGGUAUGAUAAUUAAUUAUCAUACCAUAGACAAAGAAUAAUAAUACUGACUUUCAAAGCAAAAACAGCAAAUAAAAAAGGAGCAAAGCAACCAUUAUUCGUUGCUUCGCUCCUUUUCAGCUUUACAAGUGUAUGCUGACUAUAUCUUAUUUA (((((((.......(((((((..(((((.......(((((((((((((......)).)))).((((((((((..(((........))).)))).))))))....................)))))))........)))))..)))))))...(((((((....(((..(((..(((((((.....)))))))..)))..))))))))))............(((((((.((.(((..(((((......(((((((....))))))).(((((((((((((((((.(((....))).)))))))))))))))))...)))))..))).)).))))))).......))))))).....((((((.((((((((.(((((((........))))))).))))))))(((((..(((....))).))))).......)))))). (-109.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAAGAUAUAGUCAGCAUACACUUGUAAAGCUGAAAAGGAGCGAAGCAACGAAUAAUGGUUGCUUUGCUCCUUUUUUAUUUGCUGUUUUUGCUUUGAAAGUCAGUAUUAUUAUUCUUUGUCUAUGGUAUGAUAAUUAAUUAUCAUACCGAUGUUAAUCAAUUAUCAUACCGAUGAUAAUGCAUUAUCAUAUUGAUGACAAUCAAUUAUCAUACUGAUGAUAAAGUAUUAUUAUACAGAUAAACCGAAAAAACUUUCAGCUUCUUUUGCUAUUCUUGAGGUACAACGUUCUGCUAAAAUCCUAAAUUUUAGGUAUUGUGUGAGUAAGUGAAUGAUGGUACCUUUGCAUUCUAAAAAACAUAUUAUCAAUAAAAGGCUGAACACUAAGAGAAGGUUCACAAUACUUUAGUAUAAGAAAUUAACAAUUAAAAGAACAAAA (((((((((.....(((((.(((....)))..))))).(((((((((((((((........)))))))))))))))))))))))).(((((((...((((((((.((((....)))).(((((((..((((((((((((.((((.(((....))).)))).)))))))))))).((((((((((.(((((((..((((((.......)))))).....))))))).))))))))))..)))))))........)))))))).(((((.(((((.....(((((((..(((((((((..(((((((.....)))).))).....))))...)))))...))))))).................................(((((.((......)))))))........))))).)))))............)))))))... (-115.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 300 258 230 188 pint:PI1124|5end_possible_nucleoside-diphosphate_sugar_epimerase_1049524..1049754_POSITIVE 293 403 362 151 115 pint:PI1672|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587027..1587257_POSITIVE 292 75 31 65 22 pint:PI0442|5end_50S_ribosomal_protein_L1_411644..411874_POSITIVE 290 425 385 178 141 pint:PI0651|5end_HD_superfamily_hydrolase_592270..592500_POSITIVE 289 409 372 148 115 pint:PI0360|5end_conserved_hypothetical_protein_328758..328988_POSITIVE 281 102 62 82 39 pint:PI1151|5end_hypothetical_protein_1076114..1076344_POSITIVE 276 409 367 192 159 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 273 100 56 222 160 pint:PI2111|5end_conserved_hypothetical_protein_2062771..2063001_POSITIVE 273 258 211 153 110 pint:PI1732|5end_hypothetical_protein_1651878..1652108_POSITIVE 269 420 374 68 11 pint:PI0633|5end_possible_preprotein_translocase,_YajC_subunit_579671..579901_POSITIVE 265 428 385 175 120 pint:PI0153|5end_IS1249-related_transposase_145930..146160_POSITIVE 262 426 385 172 120 pint:PI1292|5end_conserved_hypothetical_protein_1206106..1206336_POSITIVE 262 278 232 227 187 pint:PI0121|5end_outer_membrane_protein,_ompH_family_112625..112855_POSITIVE 261 428 385 140 87 pint:PI0414|5end_hypothetical_protein_384327..384557_POSITIVE 258 100 61 79 28 pint:PI0755|5end_hypothetical_protein_686691..686921_POSITIVE 258 407 385 213 190 pint:PI0127|5end_conserved_hypothetical_protein_118683..118913_POSITIVE 257 411 377 41 2 pint:PI1189|5end_conserved_hypothetical_protein_1107114..1107344_POSITIVE 257 397 366 123 79 pint:PI1009|5end_cytochrome_c_nitrite_reductase,_large_subunit_929342..929572_POSITIVE 256 418 383 60 21 pint:PI1811|5end_conserved_hypothetical_protein_1749518..1749748_POSITIVE 254 430 386 209 170 pint:PI1928|5end_conserved_hypothetical_protein_1871996..1872226_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 403 362 70 34 pint:PI1670|3end_hypothetical_protein_1587026..1587176_POSITIVE 289 409 372 145 112 pint:PI0359|3end_hypothetical_protein_328835..328985_POSITIVE 289 435 391 81 42 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 273 258 211 61 18 pint:PI1731|3end_formate--tetrahydrofolate_ligase_1651866..1652016_POSITIVE 270 403 367 148 115 pint:PI0588|3end_hypothetical_protein_535425..535575_POSITIVE 270 403 367 70 37 pint:PI0587|3end_conserved_hypothetical_protein_535347..535497_POSITIVE 265 428 385 149 94 pint:PI0152|3end_DNA_mismatch_endonuclease_vsr_145984..146134_POSITIVE 262 405 369 116 80 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 258 407 385 39 16 pint:PI0126|3end_conserved_hypothetical_protein_118589..118739_POSITIVE 257 411 377 92 53 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE 252 415 374 130 85 pint:PI1264|3end_hypothetical_protein_1185074..1185224_POSITIVE 244 418 373 137 95 pint:PI1514|3end_tRNA_nucleotidyltransferase/poly(A)_polymerase_1434072..1434222_POSITIVE 244 420 375 147 101 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 244 439 392 83 30 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE 242 405 367 57 16 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 242 399 358 60 14 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE 238 410 370 99 52 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 238 399 351 128 80 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE 235 407 376 139 104 pint:PI0974|3end_hypothetical_protein_899591..899741_POSITIVE 235 419 374 63 10 pint:PI0839|3end_conserved_hypothetical_protein_774210..774360_POSITIVE