Origin IGS: ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag .........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 ctgtttttggtttagtaaatatttagttgtttaacaattagcttattcatcaacttcagtaattaatacattagattaacaacaagtttattcatagttgccatatcataaaactcacttaaacctcatactactataaagataagataaatatgatgacctcgcaaagatacaaataaaatgataaaaacctattaatttaaaagttttttttgaaattttatctccattagtgcgaactacggcgaaaacagatgcgctaacagataggttttcaagcatttcccgccactttaaaacaa Mask Tandem Repeat Region ================================================ ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag Find is-nt database================================================ Query_seq: PI0130:PI0131|PI0130:PI0131:hypothetical protein:conserved hypothetical protein (possible outer membrane lipoprotein):->->:122328..122629 302 ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0130:PI0131|PI0130:PI0131:hypothetical protein:conserved hypothetical protein (possible outer membrane lipoprotein):->->:122328..122629 302 ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0130:PI0131|PI0130:PI0131:hypothetical protein:conserved hypothetical protein (possible outer membrane lipoprotein):->->:122328..122629 302 ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 21 End: 185 .................... M L E N L S V S A S V F A V V R T N G D K I S K K T F K L I G F Y H F I C I F A R S S Y L S Y L Y S S M R F K ..................................................................................................................... Protein_Len: 36 Strand: - Start: 2 End: 109 . T K F H R S I S S F R D T L A D T K A T T R V L P S L I E F F V K L N M ................................................................................................................................................................................................. ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag 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: 81 Start: 135 End: 164 ......................................................................................................................................TTTGCGAGGTCATCATATTTATCTTATCTT.......................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0130:PI0131|PI0130:PI0131:hypothetical protein:conserved hypothetical protein (possible outer membrane lipoprotein):->->:122328..122629 302 ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag Intra-Species Hit: Count: 1 Min: 1 Max: 302 Len: 302 Subject: pint_PI0130_PI0131|hypothetical protein:conserved hypothetical protein (possible outer membrane lipoprotein)|POSITIVE:POSITIVE|[122328,122629]|302 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 302 Query Start:1 Query End:302 Subject Strand: POSITIVE Subject Start: 1 Subject End: 302 ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcnnnnnnnncttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag ttgttttaaagtggcgggaaatgcttgaaaacctatctgttagcgcatctgttttcgccgtagttcgcactaatggagataaaatttcaaaaaaaacttttaaattaataggtttttatcattttatttgtatctttgcgaggtcatcatatttatcttatctttatagtagtatgaggtttaagtgagttttatgatatggcaactatgaataaacttgttgttaatctaatgtattaattactgaagttgatgaataagctaattgttaaacaactaaatatttactaaaccaaaaacag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUUAAAGUGGCGGGAAAUGCUUGAAAACCUAUCUGUUAGCGCAUCUGUUUUCGCCGUAGUUCGCACUAAUGGAGAUAAAAUUUCAAAAAAAACUUUUAAAUUAAUAGGUUUUUAUCAUUUUAUUUGUAUCUUUGCGAGGUCAUCAUAUUUAUCUUAUCUUUAUAGUAGUAUGAGGUUUAAGUGAGUUUUAUGAUAUGGCAACUAUGAAUAAACUUGUUGUUAAUCUAAUGUAUUAAUUACUGAAGUUGAUGAAUAAGCUAAUUGUUAAACAACUAAAUAUUUACUAAACCAAAAACAG ((((((..((.((((..((((((..((((((((((((((((((.((..(((.........)))...)).)))))))).....(((((.(((......))).)))))..)))))))))).)))))).((((((....)))))).......((((((((....((((((((((((((.(((((..((..(((((..(.(((.(....)))).)..)))))..))...)))))...))))).)))).)))))..)))))))).)))).))...)))))).......................... (-56.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUUUUGGUUUAGUAAAUAUUUAGUUGUUUAACAAUUAGCUUAUUCAUCAACUUCAGUAAUUAAUACAUUAGAUUAACAACAAGUUUAUUCAUAGUUGCCAUAUCAUAAAACUCACUUAAACCUCAUACUACUAUAAAGAUAAGAUAAAUAUGAUGACCUCGCAAAGAUACAAAUAAAAUGAUAAAAACCUAUUAAUUUAAAAGUUUUUUUUGAAAUUUUAUCUCCAUUAGUGCGAACUACGGCGAAAACAGAUGCGCUAACAGAUAGGUUUUCAAGCAUUUCCCGCCACUUUAAAACAA .((((((((((...(((......((((((.....))))))((....((((((......(((((((......((((((.......))))))....)))))))..((((.................................)))).........))))))....)).....))).....(((((...((((((((((......((((((((....)))))))).......((((((((..(....).(....)...))))))))..))))))))))....)))))...))))....)))))). (-42.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 59 13 167 122 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 325 59 13 55 10 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 317 78 32 49 12 pint:PI2158|5end_glycosyl_transferase,_group_2_family_protein_2104392..2104622_POSITIVE 316 68 22 79 36 pint:PI0642|5end_thioredoxin_family_protein_584672..584902_POSITIVE 309 67 24 149 108 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 307 59 11 229 183 pint:PI1671|5end_hypothetical_protein_1586397..1586627_POSITIVE 300 58 12 43 1 pint:PI1156|5end_possible_glycerate_kinase_family_protein_1080583..1080813_POSITIVE 298 69 22 75 25 pint:PI1364|5end_dipeptidyl_peptidase_IV_1281862..1282092_POSITIVE 297 37 2 52 16 pint:PI0569|5end_phosphoglycerate_kinase_513297..513527_POSITIVE 297 69 22 163 119 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 292 67 21 151 91 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 291 50 1 164 116 pint:PI1470|5end_hypothetical_protein_1394818..1395048_POSITIVE 289 68 43 180 148 pint:PI1883|5end_conserved_hypothetical_protein;_possible_surface_protein_1824874..1825104_POSITIVE 288 47 3 151 111 pint:PI0992|5end_RNA_polymerase_sigma-70_factor_916456..916686_POSITIVE 288 59 15 204 156 pint:PI0444|5end_50S_ribosomal_protein_L7/L12_412933..413163_POSITIVE 288 59 15 197 149 pint:PI0445|5end_conserved_hypothetical_protein_412926..413156_POSITIVE 286 79 33 157 107 pint:PI0273|5end_hypothetical_protein_262956..263186_POSITIVE 286 79 33 57 7 pint:PI0274|5end_conserved_hypothetical_protein_262856..263086_POSITIVE 286 52 13 61 8 pint:PI0045|5end_thiamine_biosynthesis_protein_43768..43998_POSITIVE 284 60 13 173 113 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 47 9 89 51 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 305 69 21 69 23 pint:PI1636|3end_hypothetical_protein_1554823..1554973_POSITIVE 298 69 22 55 5 pint:PI1363|3end_hypothetical_protein_1281922..1282072_POSITIVE 291 50 1 64 16 pint:PI1468|3end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1394798..1394948_POSITIVE 288 47 3 74 34 pint:PI0991|3end_conserved_hypothetical_protein_916459..916609_POSITIVE 288 59 15 141 93 pint:PI0443|3end_50S_ribosomal_protein_L10_412950..413100_POSITIVE 286 79 33 64 14 pint:PI0272|3end_conserved_hypothetical_protein_262943..263093_POSITIVE 286 52 13 70 17 pint:PI0044|3end_thiamine_biosynthetic_enzyme_43857..44007_POSITIVE 283 58 13 67 24 pint:PI1910|3end_hypothetical_protein_1855965..1856115_POSITIVE 283 78 31 150 123 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 283 59 11 108 58 pint:PI1398|3end_probable_imidazolonepropionase_1320672..1320822_POSITIVE 281 68 29 148 104 pint:PI1979|3end_conserved_hypothetical_protein_1937327..1937477_POSITIVE 276 60 15 142 100 pint:PI2090|3end_thioesterase_family_protein_2048066..2048216_POSITIVE 271 69 23 112 64 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 268 78 37 34 1 pint:PI2157|3end_xanthosine_triphosphate_pyrophosphatase,_HAM1_family_2104457..2104607_POSITIVE 268 70 21 74 23 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 266 76 37 63 27 pint:PI1184|3end_conserved_hypothetical_protein_1106163..1106313_POSITIVE 263 44 16 123 98 pint:PI2092|3end_hypothetical_protein_2049406..2049556_POSITIVE 262 68 21 55 4 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE 261 79 33 138 88 pint:PI0421|3end_hypothetical_protein_387774..387924_POSITIVE