Origin IGS: taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagaagaaaaagcagaaattgcccctaatcgggtagcttactttctctaaaactttggaaacaacgcttaaaacattcattttctatactttggggacaaaggtacggcaaaaaataggattaatcaagttttactaccta Mask Tandem Repeat Region ================================================ taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt Find is-nt database================================================ Query_seq: PI1846:PI1847|PI1846:PI1847:hypothetical protein:conserved hypothetical protein; possible integral membrane protein:->->:1792004..1792145 142 taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1846:PI1847|PI1846:PI1847:hypothetical protein:conserved hypothetical protein; possible integral membrane protein:->->:1792004..1792145 142 taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1846:PI1847|PI1846:PI1847:hypothetical protein:conserved hypothetical protein; possible integral membrane protein:->->:1792004..1792145 142 taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt Predict ORF larger than 30AA ================================================ taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt 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================================================ taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1846:PI1847|PI1846:PI1847:hypothetical protein:conserved hypothetical protein; possible integral membrane protein:->->:1792004..1792145 142 taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: pint_PI1846_PI1847|hypothetical protein:conserved hypothetical protein; possible integral membrane protein|POSITIVE:POSITIVE|[1792004,1792145]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt taggtagtaaaacttgattaatcctattttttgccgtacctttgtccccaaagtatagaaaatgaatgttttaagcgttgtttccaaagttttagagaaagtaagctacccgattaggggcaatttctgctttttcttcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUAGUAAAACUUGAUUAAUCCUAUUUUUUGCCGUACCUUUGUCCCCAAAGUAUAGAAAAUGAAUGUUUUAAGCGUUGUUUCCAAAGUUUUAGAGAAAGUAAGCUACCCGAUUAGGGGCAAUUUCUGCUUUUUCUUCUUU ..((.(((((..(((((...((..((((((((...((((.((((....)))))))))))))))).))...)))))..))))).)).(((....((((((((((.....(((.....)))........)))))))))).))). (-24.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAAGAAAAAGCAGAAAUUGCCCCUAAUCGGGUAGCUUACUUUCUCUAAAACUUUGGAAACAACGCUUAAAACAUUCAUUUUCUAUACUUUGGGGACAAAGGUACGGCAAAAAAUAGGAUUAAUCAAGUUUUACUACCUA .....(((((((((......(((((......)))))))))..))))).((((((((((....))...........((((((((((..(((((((....)))).)))..)...))))).)))).....))))))))....... (-24.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 140 94 63 15 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 269 140 91 163 102 pint:PI2011|5end_hypothetical_protein_1970429..1970659_POSITIVE 267 129 93 115 66 pint:PI1178|5end_histidyl-tRNA_synthetase_1099249..1099479_POSITIVE 266 139 94 221 155 pint:PI2087|5end_dihydropicolinate_reductase_2043423..2043653_POSITIVE 262 134 100 49 15 pint:PI1511|5end_hypothetical_protein_1429580..1429810_POSITIVE 258 132 93 208 169 pint:PI0198|5end_hypothetical_protein_190719..190949_POSITIVE 255 62 22 120 72 pint:PI0657|5end_conserved_hypothetical_protein_601179..601409_POSITIVE 252 130 105 140 116 pint:PI0190|5end_3-dehydroquinate_dehydratase_II_180618..180848_POSITIVE 241 140 117 159 137 pint:PI0889|5end_pyruvate_kinase_818758..818988_POSITIVE 238 140 102 209 162 pint:PI1621|5end_hypothetical_protein_1545424..1545654_POSITIVE 237 121 82 231 188 pint:PI1772|5end_pullulanase_1702257..1702487_POSITIVE 237 106 61 71 11 pint:PI1062|5end_TPR_repeat_protein_980020..980250_POSITIVE 237 130 96 82 40 pint:PI0661|5end_hypothetical_protein_603956..604186_POSITIVE 235 93 53 97 56 pint:PI1684|5end_dimethyladenosine_transferase_1601073..1601303_POSITIVE 235 138 95 90 43 pint:PI0938|5end_hypothetical_protein_869345..869575_POSITIVE 235 132 95 88 44 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 232 140 99 206 172 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 231 137 111 137 116 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 230 119 76 59 25 pint:PI0810|5end_hypothetical_protein_746743..746973_POSITIVE 230 119 76 54 20 pint:PI0811|5end_protease/hemagglutinin_PrtT,_streptopain_family_746738..746968_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 140 94 60 12 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 317 130 81 120 69 pint:PI0692|3end_iron_compound_ABC_transporter,_permease_protein_628269..628419_POSITIVE 271 120 76 88 42 pint:PI0891|3end_transketolase_822905..823055_POSITIVE 259 137 91 56 9 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 244 123 94 139 102 pint:PI2086|3end_signal_peptidase_I_2043450..2043600_POSITIVE 237 130 96 43 1 pint:PI0660|3end_conserved_hypothetical_protein_603997..604147_POSITIVE 236 47 2 41 2 pint:PI2036|3end_hypothetical_protein_1989516..1989666_POSITIVE 235 138 95 129 82 pint:PI0936|3end_conserved_hypothetical_protein_869464..869614_POSITIVE 235 132 95 88 44 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 232 76 35 132 101 pint:PI0140|3end_conserved_hypothetical_protein_132106..132256_POSITIVE 231 137 111 114 93 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 227 121 88 97 61 pint:PI0404|3end_integrase_372526..372676_POSITIVE 217 60 13 135 81 pint:PI2067|3end_hypothetical_protein_2028337..2028487_POSITIVE 217 130 85 140 84 pint:PI0830|3end_conserved_hypothetical_protein_768206..768356_POSITIVE 217 68 33 93 63 pint:PI0363|3end_hypothetical_protein_333760..333910_POSITIVE 216 130 87 133 78 pint:PI1750|3end_sulfate_transporter_1673896..1674046_POSITIVE 215 130 105 122 93 pint:PI0747|3end_possible_mobilization_protein_676702..676852_POSITIVE 214 140 93 96 44 pint:PI1827|3end_peptidase,_M23/M37_family,_N-terminal_1768602..1768752_POSITIVE 213 122 96 130 103 pint:PI1728|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_1647658..1647808_POSITIVE 213 45 14 41 5 pint:PI0440|3end_transcription_antiterminator_411204..411354_POSITIVE