Origin IGS: taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtgtagtaaccaaatcgctctcctgtgttggctaacgccaatgcataaagacttttaggttgtccttcgaacataattttaaacttttaattttgttattaattgatttta Mask Tandem Repeat Region ================================================ taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc Find is-nt database================================================ Query_seq: PI1312:PI1313|PI1312:PI1313:conserved hypothetical protein:possible POT family (proton-dependent oligopeptide transport family):->->:1229738..1229849 112 taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1312:PI1313|PI1312:PI1313:conserved hypothetical protein:possible POT family (proton-dependent oligopeptide transport family):->->:1229738..1229849 112 taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1312:PI1313|PI1312:PI1313:conserved hypothetical protein:possible POT family (proton-dependent oligopeptide transport family):->->:1229738..1229849 112 taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc Predict ORF larger than 30AA ================================================ taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc 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================================================ taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1312:PI1313|PI1312:PI1313:conserved hypothetical protein:possible POT family (proton-dependent oligopeptide transport family):->->:1229738..1229849 112 taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: pint_PI1312_PI1313|conserved hypothetical protein:possible POT family (proton-dependent oligopeptide transport family)|POSITIVE:POSITIVE|[1229738,1229849]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc taaaatcaattaataacaaaattaaaagtttaaaattatgttcgaaggacaacctaaaagtctttatgcattggcgttagccaacacaggagagcgatttggttactacacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUCAAUUAAUAACAAAAUUAAAAGUUUAAAAUUAUGUUCGAAGGACAACCUAAAAGUCUUUAUGCAUUGGCGUUAGCCAACACAGGAGAGCGAUUUGGUUACUACACC ...(((((((((((......))))).............(((((.((((((.........)))))).((..(((((....)))))..))...)))))..))))))........ (-17.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGUAGUAACCAAAUCGCUCUCCUGUGUUGGCUAACGCCAAUGCAUAAAGACUUUUAGGUUGUCCUUCGAACAUAAUUUUAAACUUUUAAUUUUGUUAUUAAUUGAUUUUA ((.....(((((.((..(.(((..(((((((((....)))))))))...))))..)).))))).))....((((.((((..........)))).)))).............. (-20.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 104 67 208 166 pint:PI0698|5end_conserved_hypothetical_protein_635372..635602_POSITIVE 300 97 59 86 53 pint:PI1009|5end_cytochrome_c_nitrite_reductase,_large_subunit_929342..929572_POSITIVE 284 108 62 143 89 pint:PI1476|5end_acyl-CoA_synthase/O-succinylbenzoic_acid-CoA_ligase_1397699..1397929_POSITIVE 278 93 53 172 132 pint:PI1343|5end_conserved_hypothetical_protein_1257782..1258012_POSITIVE 277 109 65 99 45 pint:PI0384|5end_probable_radical_SAM_domain_protein_352884..353114_POSITIVE 271 96 67 52 29 pint:PI0047|5end_phosphomethylpyrimidine_kinase_45964..46194_POSITIVE 266 104 67 84 37 pint:PI1583|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase_(AICAR)/IMP_cyclohydrolase_(ATIC)_1510530..1510760_POSITIVE 262 107 66 60 7 pint:PI1140|5end_ABC_transporter,_ATP-binding_protein_1067373..1067603_POSITIVE 259 107 73 44 5 pint:PI2013|5end_hypothetical_protein_1972329..1972559_POSITIVE 259 102 67 171 138 pint:PI2014|5end_conserved_hypothetical_protein_1971471..1971701_POSITIVE 258 85 44 190 141 pint:PI0505|5end_mobilization_protein_464578..464808_POSITIVE 258 85 44 71 22 pint:PI0504|5end_hypothetical_protein_464459..464689_POSITIVE 257 104 80 165 139 pint:PI1479|5end_xanthine_phosphoribosyltransferase_1402098..1402328_POSITIVE 253 85 41 215 168 pint:PI1000|5end_conserved_hypothetical_protein_923332..923562_POSITIVE 252 110 67 73 22 pint:PI2087|5end_dihydropicolinate_reductase_2043423..2043653_POSITIVE 252 101 66 30 3 pint:PI0694|5end_Na+/dicarboxylate_or_sulfate_symporter_629745..629975_POSITIVE 251 79 38 44 3 pint:PI1986|5end_hypothetical_protein_1940863..1941093_POSITIVE 251 106 66 227 187 pint:PI0320|5end_probable_cobalamin_adenosyltransferase_302027..302257_POSITIVE 248 109 61 172 130 pint:PI1831|5end_conserved_hypothetical_protein_1770298..1770528_POSITIVE 248 100 51 223 177 pint:PI0844|5end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_777793..778023_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 104 67 96 54 pint:PI0697|3end_5'-nucleotidase_family_protein_635340..635490_POSITIVE 300 110 61 151 95 pint:PI0391|3end_conserved_hypothetical_protein_358216..358366_POSITIVE 278 93 53 109 69 pint:PI1342|3end_conserved_hypothetical_protein_1257799..1257949_POSITIVE 271 96 67 52 29 pint:PI0046|3end_thiamine_monophosphate_synthase_(thiamine-phosphate_pyrophosphorylase)_46044..46194_POSITIVE 261 108 62 107 56 pint:PI0779|3end_predicted_TPR-repeat-containing_protein_715800..715950_POSITIVE 257 104 80 131 105 pint:PI1478|3end_hypothetical_protein_1402144..1402294_POSITIVE 255 106 63 78 34 pint:PI1838|3end_conserved_hypothetical_protein_1782028..1782178_POSITIVE 253 85 41 139 92 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 250 83 57 151 126 pint:PI2174|3end_hypothetical_protein_2114969..2115119_POSITIVE 246 97 57 110 74 pint:PI0736|3end_transcriptional_regulator,_TetR_family_671271..671421_POSITIVE 245 89 43 143 105 pint:PI0640|3end_conserved_hypothetical_protein_583821..583971_POSITIVE 243 98 51 70 6 pint:PI0844|3end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_778316..778466_POSITIVE 241 97 61 147 110 pint:PI1752|3end_conserved_hypothetical_protein_1681270..1681420_POSITIVE 241 103 64 62 22 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE 239 98 61 59 23 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 233 84 45 59 10 pint:PI0625|3end_possible_membrane_transport_protein_574353..574503_POSITIVE 232 107 66 141 98 pint:PI1349|3end_polysaccharide_export_protein_1265720..1265870_POSITIVE 231 105 63 142 91 pint:PI0465|3end_50S_ribosomal_protein_L22_435793..435943_POSITIVE 230 106 67 67 27 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 228 96 67 136 101 pint:PI0767|3end_possible_TonB-dependent_receptor_704025..704175_POSITIVE