Origin IGS: taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta .........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 taaggagaaatattatccttttcttaaaaatatttcctaaaaaaagcactttttttgttagaaatgatgcttatataaaaaattatgcttacttttgccacataatttgatatgttagtaacttactaattacaagataaaagataatttgattgtataataaaataaaagttatgaaaaaattttta Mask Tandem Repeat Region ================================================ taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta Find is-nt database================================================ Query_seq: PI1717:PI1718|PI1717:PI1718:major outer membrane protein:DNA mismatch repair protein:->->:1633949..1634136 188 taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1717:PI1718|PI1717:PI1718:major outer membrane protein:DNA mismatch repair protein:->->:1633949..1634136 188 taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1717:PI1718|PI1717:PI1718:major outer membrane protein:DNA mismatch repair protein:->->:1633949..1634136 188 taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 82 End: 177 ................................................................................. I I H C F Y A Y N K I Y A D N R V F F T S K K P F I K L F L I M ........... taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta 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: 83 Start: 8 End: 37 .......TTTTTCATAACTTTTATTTTATTATACAAT....................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1717:PI1718|PI1717:PI1718:major outer membrane protein:DNA mismatch repair protein:->->:1633949..1634136 188 taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta Intra-Species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: pint_PI1717_PI1718|major outer membrane protein:DNA mismatch repair protein|POSITIVE:POSITIVE|[1633949,1634136]|188 HSP 1 e-value: 2.0E-77 bit: 289.0 Len: 188 Query Start:1 Query End:188 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacnnnnnnngtgcnnnnnnnaggaaatatttttaagaaaaggataatatttctcctta taaaaattttttcataacttttattttattatacaatcaaattatcttttatcttgtaattagtaagttactaacatatcaaattatgtggcaaaagtaagcataattttttatataagcatcatttctaacaaaaaaagtgctttttttaggaaatatttttaagaaaaggataatatttctcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUUUUUUCAUAACUUUUAUUUUAUUAUACAAUCAAAUUAUCUUUUAUCUUGUAAUUAGUAAGUUACUAACAUAUCAAAUUAUGUGGCAAAAGUAAGCAUAAUUUUUUAUAUAAGCAUCAUUUCUAACAAAAAAAGUGCUUUUUUUAGGAAAUAUUUUUAAGAAAAGGAUAAUAUUUCUCCUUA ........................................((((((((((.(((((...((((((...)))))).(((..(((((((((.((....))..)))))))))..))).........((((((...(((((((....))))))).)))))).....)))))))))))))))........... (-24.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAGAAAUAUUAUCCUUUUCUUAAAAAUAUUUCCUAAAAAAAGCACUUUUUUUGUUAGAAAUGAUGCUUAUAUAAAAAAUUAUGCUUACUUUUGCCACAUAAUUUGAUAUGUUAGUAACUUACUAAUUACAAGAUAAAAGAUAAUUUGAUUGUAUAAUAAAAUAAAAGUUAUGAAAAAAUUUUUA ((((((((..........))))))))....((((((.((((((((....))))))))...))))))....((((((((.(((((((.(((..(((((..(((((......)))))(((((...)))))....)))))...))))))))))..)))))))).....((((((((.......)))))))) (-23.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 202 58 11 134 87 pint:PI1518|5end_outer_membrane_protein_oprM_precursor,_multidrug_resistance_protein_1438922..1439152_POSITIVE 199 110 66 226 183 pint:PI0454|5end_hypothetical_protein_426653..426883_POSITIVE 196 126 83 64 21 pint:PI1108|5end_conserved_hypothetical_protein_1031456..1031686_POSITIVE 182 122 87 170 136 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 182 106 65 167 135 pint:PI0017|5end_thiol-disulfide_isomerase;_thioredoxin_21733..21963_POSITIVE 178 113 75 107 66 pint:PI0161|5end_possible_TonB_receptor_153364..153594_POSITIVE 177 100 59 167 122 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 177 100 59 109 64 pint:PI0565|5end_hypothetical_protein_511479..511709_POSITIVE 177 104 66 144 100 pint:PI0275|5end_hypothetical_protein_263138..263368_POSITIVE 176 152 118 161 126 pint:PI1978|5end_hypothetical_protein_1934615..1934845_POSITIVE 176 152 118 225 190 pint:PI1976|5end_hypothetical_protein_1932993..1933223_POSITIVE 173 102 61 156 115 pint:PI0308|5end_conserved_hypothetical_protein_290587..290817_POSITIVE 171 128 89 112 70 pint:PI2122|5end_conserved_hypothetical_protein_2069744..2069974_POSITIVE 169 110 84 142 113 pint:PI1603|5end_hypothetical_protein_1533779..1534009_POSITIVE 169 124 83 86 44 pint:PI1535|5end_response_regulator_1454096..1454326_POSITIVE 168 127 84 148 112 pint:PI1553|5end_hypothetical_protein_1469464..1469694_POSITIVE 166 164 123 155 114 pint:PI2012|5end_hypothetical_protein_1970807..1971037_POSITIVE 166 110 62 53 7 pint:PI1373|5end_purine_nucleoside_phosphorylase_(PNP)_1294031..1294261_POSITIVE 166 155 111 201 148 pint:PI1132|5end_DnaJ_heat_shock_protein_(Hsp40)_1058434..1058664_POSITIVE 165 53 11 134 87 pint:PI0368|5end_hypothetical_protein_339582..339812_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 202 58 11 105 58 pint:PI1517|3end_AcrB/AcrD_family_multidrug_resistance_protein_1438973..1439123_POSITIVE 196 126 83 64 21 pint:PI1107|3end_conserved_hypothetical_protein_1031536..1031686_POSITIVE 189 94 60 60 27 pint:PI0233|3end_membrane_protein,_possible_exporter_233771..233921_POSITIVE 182 106 65 79 47 pint:PI0016|3end_magnesium_chelatase,_subunit_ChlI_21725..21875_POSITIVE 177 104 66 113 69 pint:PI0274|3end_conserved_hypothetical_protein_263187..263337_POSITIVE 176 152 118 85 50 pint:PI1977|3end_hypothetical_protein_1934619..1934769_POSITIVE 176 152 118 85 50 pint:PI1975|3end_conserved_hypothetical_protein_1932933..1933083_POSITIVE 172 98 54 61 8 pint:PI0663|3end_possible_transcriptional_regulator_606543..606693_POSITIVE 169 110 84 102 73 pint:PI1602|3end_conserved_hypothetical_protein;_possible_internalin-related_protein_1533819..1533969_POSITIVE 169 124 83 76 34 pint:PI1534|3end_ATPase/GTPase_1454166..1454316_POSITIVE 168 114 86 113 84 pint:PI1435|3end_D12_class_N6_adenine-specific_DNA_methyltransferase_1355613..1355763_POSITIVE 165 104 83 21 2 pint:PI1542|3end_mobilization_protein_1462866..1463016_POSITIVE 165 53 11 112 65 pint:PI0367|3end_hypothetical_protein_339640..339790_POSITIVE 163 122 85 84 32 pint:PI0455|3end_hypothetical_protein_428502..428652_POSITIVE 162 153 118 87 53 pint:PI1733|3end_hypothetical_protein_1652437..1652587_POSITIVE 160 110 70 113 77 pint:PI0309|3end_hypothetical_protein_291729..291879_POSITIVE 156 154 124 86 55 pint:PI2080|3end_hypothetical_protein_2038298..2038448_POSITIVE 156 105 64 126 85 pint:PI0408|3end_hypothetical_protein_374728..374878_POSITIVE 154 58 11 114 70 pint:PI0837|3end_conserved_hypothetical_protein_772681..772831_POSITIVE 153 125 90 73 35 pint:PI1856|3end_nicotinate-nucleotide_adenylyltransferase_1803885..1804035_POSITIVE