Origin IGS: agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg .........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 cgttgcgatggcactcataaggaagatatactgacgtttcatgactttatacttttaaattgttatacttatttttcattgtttatgctgcaaatatagcggtaattccccatacagccaagggcgtatgcctataattgggcggaaaatccctactctttcaaatgtgcggaaagttgtattgtaatataaaatcatcttttataggtatgtaatgtttacagtaaacactgcttacacccttattttagggcattctttgttttatttaatacacaaagacaactatttttgtcatatcagtattatattgccaccctaagaagaatatataataacaaattgacagaataaattcaatagagtgaaaccaagggaaaagaacactttatgacaatattttactaacttttgggtattgtctgttattttataagtaaatacctttgcacgcattaaattaatataccatattatatgaaacgagttttaattctattttcaggattgctttgtgccgttatgtct Mask Tandem Repeat Region ================================================ agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg Find is-nt database================================================ Query_seq: PI0049:PI0050|PI0049:PI0050:outer membrane receptor protein (iron transport):conserved hypothetical protein:->->:51151..51678 528 agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0049:PI0050|PI0049:PI0050:outer membrane receptor protein (iron transport):conserved hypothetical protein:->->:51151..51678 528 agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0049:PI0050|PI0049:PI0050:outer membrane receptor protein (iron transport):conserved hypothetical protein:->->:51151..51678 528 agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 52 End: 207 ................................................... M I W Y I N L M R A K V F T Y K I T D N T Q K L V K Y C H K V F F S L G F T L L N L F C Q F V I I Y S S ................................................................................................................................................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 168 End: 257 ....................................................................................................................................................................... M E F I L S I C Y Y I F F L G W Q Y N T D M T K I V V F V Y ............................................................................................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 331 End: 450 .......................................................................................................................................................................................................................................................................................................................................... M I L Y Y N T T F R T F E R V G I F R P I I G I R P W L Y G E L P L Y L Q H K Q .............................................................................. Protein_Len: 42 Strand: - Start: 345 End: 470 ........................................................................................................................................................................................................................................................................................................................................................ L V V K R V N S L T P I K R G I I P M R G Q S Y P S N G S Y K C C L C H F I L I V M .......................................................... Protein_Len: 42 Strand: - Start: 210 End: 335 ................................................................................................................................................................................................................. P P L I I S I H C F Y N D K H I L Y F L S H G L I L T Y A T N V T F M V Y R Y F I M ................................................................................................................................................................................................. agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg 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: 84 Start: 168 End: 197 .......................................................................................................................................................................ATTGAATTTATTCTGTCAATTTGTTATTAT........................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 407 End: 436 ......................................................................................................................................................................................................................................................................................................................................................................................................................CTTGGCTGTATGGGGAATTACCGCTATATT............................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -3.3 Tail_Score: -4.21811 Start: 233 End: 248 Full_Region: ATATAATACTGATAT GACAA AAATAG TTGTC TTTGTGTATTAAATA ........................................................................................................................................................................................................................................GACAAAAATAGTTGTC........................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: PI0049:PI0050|PI0049:PI0050:outer membrane receptor protein (iron transport):conserved hypothetical protein:->->:51151..51678 528 agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg Intra-Species Hit: Count: 1 Min: 1 Max: 528 Len: 528 Subject: pint_PI0049_PI0050|outer membrane receptor protein (iron transport):conserved hypothetical protein|POSITIVE:POSITIVE|[51151,51678]|528 HSP 1 e-value: 0.0 bit: 1047.0 Len: 528 Query Start:1 Query End:528 Subject Strand: POSITIVE Subject Start: 1 Subject End: 528 agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg agacataacggcacaaagcaatcctgaaaatagaattaaaactcgtttcatataatatggtatattaatttaatgcgtgcaaaggtatttacttataaaataacagacaatacccaaaagttagtaaaatattgtcataaagtgttcttttcccttggtttcactctattgaatttattctgtcaatttgttattatatattcttcttagggtggcaatataatactgatatgacaaaaatagttgtctttgtgtattaaataaaacaaagaatgccctaaaataagggtgtaagcagtgtttactgtaaacattacatacctataaaagatgattttatattacaatacaactttccgcacatttgaaagagtagggattttccgcccaattataggcatacgcccttggctgtatggggaattaccgctatatttgcagcataaacaatgaaaaataagtataacaatttaaaagtataaagtcatgaaacgtcagtatatcttccttatgagtgccatcgcaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACAUAACGGCACAAAGCAAUCCUGAAAAUAGAAUUAAAACUCGUUUCAUAUAAUAUGGUAUAUUAAUUUAAUGCGUGCAAAGGUAUUUACUUAUAAAAUAACAGACAAUACCCAAAAGUUAGUAAAAUAUUGUCAUAAAGUGUUCUUUUCCCUUGGUUUCACUCUAUUGAAUUUAUUCUGUCAAUUUGUUAUUAUAUAUUCUUCUUAGGGUGGCAAUAUAAUACUGAUAUGACAAAAAUAGUUGUCUUUGUGUAUUAAAUAAAACAAAGAAUGCCCUAAAAUAAGGGUGUAAGCAGUGUUUACUGUAAACAUUACAUACCUAUAAAAGAUGAUUUUAUAUUACAAUACAACUUUCCGCACAUUUGAAAGAGUAGGGAUUUUCCGCCCAAUUAUAGGCAUACGCCCUUGGCUGUAUGGGGAAUUACCGCUAUAUUUGCAGCAUAAACAAUGAAAAAUAAGUAUAACAAUUUAAAAGUAUAAAGUCAUGAAACGUCAGUAUAUCUUCCUUAUGAGUGCCAUCGCAACG .........(((((.........(((....))).......(((((((((......((((((((....(((((((((..(((((((..((((((.............................))))))...((((((((.((((((...........(((((((((((..((((.(((..((.(.....).))..))).))))....)))))))).)))..))))))..)))))))).........))))))))))))))))..........(((((((......)))))))..(((((....))))).........))))).)))....(((((((((((((.........(((((.........)))))....((((((..(((..((.(((..(((....)))..))).))..)))..)))).))..((((((((...(((.....))).....))))))))..........)))))))))))))))))))..)))...............)))))......... (-102.07) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUGCGAUGGCACUCAUAAGGAAGAUAUACUGACGUUUCAUGACUUUAUACUUUUAAAUUGUUAUACUUAUUUUUCAUUGUUUAUGCUGCAAAUAUAGCGGUAAUUCCCCAUACAGCCAAGGGCGUAUGCCUAUAAUUGGGCGGAAAAUCCCUACUCUUUCAAAUGUGCGGAAAGUUGUAUUGUAAUAUAAAAUCAUCUUUUAUAGGUAUGUAAUGUUUACAGUAAACACUGCUUACACCCUUAUUUUAGGGCAUUCUUUGUUUUAUUUAAUACACAAAGACAACUAUUUUUGUCAUAUCAGUAUUAUAUUGCCACCCUAAGAAGAAUAUAUAAUAACAAAUUGACAGAAUAAAUUCAAUAGAGUGAAACCAAGGGAAAAGAACACUUUAUGACAAUAUUUUACUAACUUUUGGGUAUUGUCUGUUAUUUUAUAAGUAAAUACCUUUGCACGCAUUAAAUUAAUAUACCAUAUUAUAUGAAACGAGUUUUAAUUCUAUUUUCAGGAUUGCUUUGUGCCGUUAUGUCU ......((((((((....(((.............((((((((((.(((((.((.((((.(((((((...((((((((....((((((.(((((.((((((.....((((..((((.(((...)))))))(((((....)))))))))..(((.(((..........))).)))..))))))))))).))))))...........((((...(((((((.(((...(((((..(......((((......))))....)..)))))...............(((((......)))))......)))..)))))))...)))).))))))))....))))))).)))).)).))))).)).....((((....((((((.((((....))))..((((((((((...........))))))))))....................))))))....))))....................)))))))).....(((((((......)))))))))).))))))))...... (-108.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 430 385 107 63 pint:PI0938|5end_hypothetical_protein_869345..869575_POSITIVE 347 419 371 81 32 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 347 420 373 231 194 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 346 420 371 208 159 pint:PI1187|5end_conserved_hypothetical_protein_1106692..1106922_POSITIVE 343 429 381 229 178 pint:PI0331|5end_hypothetical_protein_311656..311886_POSITIVE 331 430 381 84 36 pint:PI0068|5end_arginine_repressor_66586..66816_POSITIVE 324 420 371 230 181 pint:PI2077|5end_hypothetical_protein_2035892..2036122_POSITIVE 313 429 393 59 28 pint:PI1247|5end_conserved_hypothetical_protein_1171630..1171860_POSITIVE 307 420 372 189 129 pint:PI1204|5end_hypothetical_protein_1124430..1124660_POSITIVE 300 413 372 209 165 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 300 395 354 64 15 pint:PI0546|5end_hypothetical_protein_497799..498029_POSITIVE 298 446 404 225 174 pint:PI1185|5end_hypothetical_protein_1106076..1106306_POSITIVE 297 420 371 193 157 pint:PI1265|5end_hypothetical_protein_1185016..1185246_POSITIVE 296 420 371 87 34 pint:PI0591|5end_adenylosuccinate_lyase_538595..538825_POSITIVE 296 420 380 59 15 pint:PI0492|5end_hypothetical_protein_451701..451931_POSITIVE 295 442 402 185 141 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 295 400 353 190 135 pint:PI1549|5end_conserved_hypothetical_protein_1467021..1467251_POSITIVE 295 438 392 52 6 pint:PI0058|5end_conserved_hypothetical_protein_56398..56628_POSITIVE 294 440 392 150 113 pint:PI1754|5end_conserved_hypothetical_protein_1681202..1681432_POSITIVE 288 421 394 231 196 pint:PI0408|5end_hypothetical_protein_374154..374384_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 430 385 146 102 pint:PI0936|3end_conserved_hypothetical_protein_869464..869614_POSITIVE 332 433 394 150 109 pint:PI0407|3end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_374147..374297_POSITIVE 307 420 372 118 58 pint:PI1203|3end_conserved_hypothetical_protein_1124439..1124589_POSITIVE 300 395 354 52 3 pint:PI0545|3end_sugar_kinase_497867..498017_POSITIVE 295 442 402 74 30 pint:PI2084|3end_hypothetical_protein_2041069..2041219_POSITIVE 295 438 392 86 40 pint:PI0057|3end_conserved_hypothetical_protein_56512..56662_POSITIVE 294 440 392 138 101 pint:PI1752|3end_conserved_hypothetical_protein_1681270..1681420_POSITIVE 294 440 392 150 113 pint:PI1753|3end_conserved_hypothetical_protein_1681282..1681432_POSITIVE 291 414 379 145 105 pint:PI0829|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_766539..766689_POSITIVE 286 431 397 100 54 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 281 419 375 75 30 pint:PI1436|3end_hypothetical_protein_1356232..1356382_POSITIVE 279 416 375 55 18 pint:PI1700|3end_hypothetical_protein_1619243..1619393_POSITIVE 277 419 371 62 11 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 276 419 378 150 109 pint:PI1852|3end_conserved_hypothetical_protein_1799321..1799471_POSITIVE 274 440 398 45 3 pint:PI1643|3end_conserved_hypothetical_protein_1562029..1562179_POSITIVE 271 430 381 144 94 pint:PI0191|3end_O-methyltransferase_181785..181935_POSITIVE 270 448 410 129 91 pint:PI1472|3end_hypothetical_protein_1395879..1396029_POSITIVE 270 448 410 80 42 pint:PI1473|3end_hypothetical_protein_1395830..1395980_POSITIVE 268 450 404 72 23 pint:PI1980|3end_conserved_hypothetical_protein_1937945..1938095_POSITIVE 268 520 484 118 77 pint:PI0476|3end_50S_ribosomal_protein_L18_440462..440612_POSITIVE