Origin IGS: acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta .........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 taattgaaaatgcaatattgaagttttcttgcttaatcccttgctactttcaaagaaaaggtttatatttgcaaccgaataataaacaatctgcaaaaacatagttaataattaataaccctaacgccccagtctcggtaaggcgttctccctttgagataggggagtcaaggagagacacttgaaacaatgaaaaacaatctattcaagaagatgt Mask Tandem Repeat Region ================================================ acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta Find is-nt database================================================ Query_seq: PI1245:PI1247|PI1245:PI1247:hypothetical protein:conserved hypothetical protein:->->:1171553..1171769 217 acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1245:PI1247|PI1245:PI1247:hypothetical protein:conserved hypothetical protein:->->:1171553..1171769 217 acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1245:PI1247|PI1245:PI1247:hypothetical protein:conserved hypothetical protein:->->:1171553..1171769 217 acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 13 End: 165 ............ M D C F S L F Q V S L L D S P I S K G E R L T E T G A L G L L I I N Y V F A D C L L F G C K Y K P F L .................................................... Protein_Len: 34 Strand: + Start: 116 End: 217 ................................................................................................................... M F L Q I V Y Y S V A N I N L F F E S S K G L S K K T S I L H F Q L Protein_Len: 33 Strand: - Start: 117 End: 215 .................................................................................................................... T K A S Q K N N P Q L Y L G K R Q F Y C P I L C S F K L I A N E M .. acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta 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: 82 Start: 149 End: 178 ....................................................................................................................................................CTTGCTACTTTCAAAGAAAAGGTTTATATT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1245:PI1247|PI1245:PI1247:hypothetical protein:conserved hypothetical protein:->->:1171553..1171769 217 acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta Intra-Species Hit: Count: 1 Min: 1 Max: 217 Len: 217 Subject: pint_PI1245_PI1247|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1171553,1171769]|217 HSP 1 e-value: 1.0E-120 bit: 430.0 Len: 217 Query Start:1 Query End:217 Subject Strand: POSITIVE Subject Start: 1 Subject End: 217 acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta acatcttcttgaatagattgtttttcattgtttcaagtgtctctccttgactcccctatctcaaagggagaacgccttaccgagactggggcgttagggttattaattattaactatgtttttgcagattgtttattattcggttgcaaatataaaccttttctttgaaagtagcaagggattaagcaagaaaacttcaatattgcattttcaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUCUUCUUGAAUAGAUUGUUUUUCAUUGUUUCAAGUGUCUCUCCUUGACUCCCCUAUCUCAAAGGGAGAACGCCUUACCGAGACUGGGGCGUUAGGGUUAUUAAUUAUUAACUAUGUUUUUGCAGAUUGUUUAUUAUUCGGUUGCAAAUAUAAACCUUUUCUUUGAAAGUAGCAAGGGAUUAAGCAAGAAAACUUCAAUAUUGCAUUUUCAAUUA .........(((((((.((((....(((.(((...(((......(((((((.((((..((((..((((......))))...))))..)))).)))))))......)))...))).))).....)))).)))))))......((((.........))))......((((((((.((((...((((((........))).))).))))))))))))... (-49.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUGAAAAUGCAAUAUUGAAGUUUUCUUGCUUAAUCCCUUGCUACUUUCAAAGAAAAGGUUUAUAUUUGCAACCGAAUAAUAAACAAUCUGCAAAAACAUAGUUAAUAAUUAAUAACCCUAACGCCCCAGUCUCGGUAAGGCGUUCUCCCUUUGAGAUAGGGGAGUCAAGGAGAGACACUUGAAACAAUGAAAAACAAUCUAUUCAAGAAGAUGU ..((((......))))......(((((((((..((.(((((((....((((((((.....(((((((((((....))))).))))))...................................((((((((......))...))))))....))))))))))))))).(((((........))))).................))..))))))))).. (-42.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 540 98 51 183 130 pint:PI1223|5end_conserved_hypothetical_protein_1143537..1143767_POSITIVE 530 109 63 173 127 pint:PI0756|5end_50S_ribosomal_protein_L7/L12_687146..687376_POSITIVE 363 101 66 228 192 pint:PI0655|5end_Na+/H+_anitporter_597290..597520_POSITIVE 346 95 51 220 161 pint:PI0576|5end_helicase,_UvrD/Rep_520226..520456_POSITIVE 314 44 3 207 169 pint:PI0127|5end_conserved_hypothetical_protein_118683..118913_POSITIVE 304 100 54 88 48 pint:PI1098|5end_conserved_hypothetical_protein_1022261..1022491_POSITIVE 303 100 57 146 100 pint:PI1913|5end_conserved_hypothetical_protein_1857104..1857334_POSITIVE 303 98 52 87 48 pint:PI0895|5end_2-oxoglutarate_oxidoreductase,_beta_subunit,_possible_ketoisovalerate_oxidoreductase,__vorA_826347..826577_POSITIVE 295 88 41 219 152 pint:PI1625|5end_conserved_hypothetical_protein;_possible_phage_transposase_1549316..1549546_POSITIVE 295 88 41 219 152 pint:PI0332|5end_conserved_hypothetical_protein_312600..312830_POSITIVE 292 119 73 161 118 pint:PI1443|5end_conserved_hypotehtical_protein;_possible_tonB-dependent_outer_membrane_receptor_1364560..1364790_POSITIVE 291 99 60 66 20 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 291 99 54 196 153 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 288 100 52 194 140 pint:PI1704|5end_50S_ribosomal_protein_L32_1621418..1621648_POSITIVE 287 99 57 171 129 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 287 99 56 202 155 pint:PI0393|5end_conserved_hypothetical_protein_358696..358926_POSITIVE 283 99 51 87 38 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 283 99 56 174 140 pint:PI0536|5end_hypothetical_protein_492163..492393_POSITIVE 281 57 15 224 179 pint:PI0514|5end_possible_cell_filamentation_protein_472408..472638_POSITIVE 278 92 54 158 112 pint:PI1179|5end_adenylosuccinate_synthetase_1100628..1100858_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 101 66 81 45 pint:PI0654|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_597223..597373_POSITIVE 346 95 51 142 83 pint:PI0575|3end_hypothetical_protein_520228..520378_POSITIVE 313 99 53 50 4 pint:PI1246|3end_conserved_hypothetical_protein;_possible_lipoprotein_1171496..1171646_POSITIVE 310 74 36 129 90 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 303 100 57 128 82 pint:PI1912|3end_possible_DNA_repair_protein_1857166..1857316_POSITIVE 302 95 51 60 10 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 298 96 65 149 111 pint:PI0407|3end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_374147..374297_POSITIVE 295 88 41 84 17 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 295 88 41 114 47 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 295 88 41 84 17 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 289 100 56 92 37 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE 287 99 57 58 16 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 284 95 60 147 107 pint:PI1606|3end_conserved_hypothetical_protein_1535565..1535715_POSITIVE 280 99 54 46 1 pint:PI1245|3end_hypothetical_protein_1171492..1171642_POSITIVE 276 99 52 145 100 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 262 100 65 69 35 pint:PI0189|3end_integrase_180437..180587_POSITIVE 261 92 52 143 96 pint:PI0936|3end_conserved_hypothetical_protein_869464..869614_POSITIVE 257 50 9 98 59 pint:PI0959|3end_uridine_kinase_891204..891354_POSITIVE 252 116 72 54 3 pint:PI0765|3end_conserved_hypothetical_protein;_possible_surface_protein_700822..700972_POSITIVE 249 100 54 45 1 pint:PI0624|3end_hypothetical_protein_574471..574621_POSITIVE