Origin IGS: aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagattttcttgttagaacttgttttttaacacggttgtaacgatgttttggtaaattttagttatatttgcaccataattataatataacgttattaaatcttaacatcaatttatt Mask Tandem Repeat Region ================================================ aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta Find is-nt database================================================ Query_seq: PI1319:PI1320|PI1319:PI1320:possible OmpA , outer membrane protein-related protein:conserved hypothetical protein:->->:1239053..1239170 118 aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1319:PI1320|PI1319:PI1320:possible OmpA , outer membrane protein-related protein:conserved hypothetical protein:->->:1239053..1239170 118 aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1319:PI1320|PI1319:PI1320:possible OmpA , outer membrane protein-related protein:conserved hypothetical protein:->->:1239053..1239170 118 aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta Predict ORF larger than 30AA ================================================ aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta 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: 6 End: 35 .....ATTGATGTTAAGATTTAATAACGTTATATT................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 33 End: 62 ................................TTTTAGTTATATTTGCACCATAATTATAAT........................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1319:PI1320|PI1319:PI1320:possible OmpA , outer membrane protein-related protein:conserved hypothetical protein:->->:1239053..1239170 118 aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: pint_PI1319_PI1320|possible OmpA , outer membrane protein-related protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1239053,1239170]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta aataaattgatgttaagatttaataacgttatattataattatggtgcaaatataactaaaatttaccaaaacatcgttacaaccgtgttaaaaaacaagttctaacaagaaaatcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAUUGAUGUUAAGAUUUAAUAACGUUAUAUUAUAAUUAUGGUGCAAAUAUAACUAAAAUUUACCAAAACAUCGUUACAACCGUGUUAAAAAACAAGUUCUAACAAGAAAAUCUA ...............((((((......((((((((...((....))...))))))))...................((((.(((..((((....)))).))).))))....)))))). (-13.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUUUUCUUGUUAGAACUUGUUUUUUAACACGGUUGUAACGAUGUUUUGGUAAAUUUUAGUUAUAUUUGCACCAUAAUUAUAAUAUAACGUUAUUAAAUCUUAACAUCAAUUUAUU ...........((((.((((((((....)))).)))).))))((((((..(((........((((((((..............))))))))........)))..))))))........ (-20.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 86 44 186 148 pint:PI0595|5end_conserved_hypothetical_protein_545571..545801_POSITIVE 266 110 63 182 132 pint:PI1431|5end_conserved_hypothetical_protein_1352079..1352309_POSITIVE 219 100 63 104 72 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 219 100 63 46 14 pint:PI0565|5end_hypothetical_protein_511479..511709_POSITIVE 216 61 23 123 78 pint:PI1621|5end_hypothetical_protein_1545424..1545654_POSITIVE 212 85 45 77 31 pint:PI0189|5end_integrase_179623..179853_POSITIVE 200 89 44 93 45 pint:PI0824|5end_large_conductance_mechanosensitive_channel_protein_763337..763567_POSITIVE 192 89 65 56 29 pint:PI0764|5end_permease_697962..698192_POSITIVE 189 89 43 231 183 pint:PI1554|5end_hypothetical_protein_1470275..1470505_POSITIVE 186 47 8 120 82 pint:PI0629|5end_heat_shock_protein_15_576629..576859_POSITIVE 186 89 43 99 55 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 185 105 67 51 10 pint:PI1849|5end_conserved_hypothetical_protein;_possible_acyltransferase_family_protein_1794916..1795146_POSITIVE 184 90 46 183 142 pint:PI0093|5end_riboflavin_biosynthesis_protein_90489..90719_POSITIVE 182 90 43 138 92 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 181 88 66 44 21 pint:PI0755|5end_hypothetical_protein_686691..686921_POSITIVE 179 110 65 183 146 pint:PI1508|5end_undecaprenol_kinase_1427288..1427518_POSITIVE 173 85 67 26 8 pint:PI0873|5end_conserved_hypothetical_protein;_possible_permease_807968..808198_POSITIVE 172 89 46 55 8 pint:PI1447|5end_probable_OPT_oligopeptide_transporter_protein_1369972..1370202_POSITIVE 171 87 42 87 24 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 169 88 62 205 184 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 100 63 144 112 pint:PI0565|3end_hypothetical_protein_511657..511807_POSITIVE 195 103 68 46 9 pint:PI1146|3end_translation_initiation_factor_IF3_1073503..1073653_POSITIVE 194 78 44 129 95 pint:PI0761|3end_hypothetical_protein_696348..696498_POSITIVE 188 89 46 46 1 pint:PI1553|3end_hypothetical_protein_1470170..1470320_POSITIVE 188 85 54 44 13 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE 186 47 8 96 58 pint:PI0628|3end_phosphoribosylglycinamide_formyltransferase_576685..576835_POSITIVE 185 105 67 70 29 pint:PI1848|3end_hypothetical_protein_1795015..1795165_POSITIVE 184 90 46 125 84 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 182 90 43 128 82 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 169 88 62 148 127 pint:PI0535|3end_hypothetical_protein_489779..489929_POSITIVE 154 92 65 144 110 pint:PI0009|3end_NAD-dependent_epimerase/dehydratase_family_protein_10674..10824_POSITIVE 151 109 76 57 29 pint:PI1563|3end_thiol:disulfide_interchange_protein_dsbD_1482815..1482965_POSITIVE 150 108 63 138 92 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 149 50 9 104 57 pint:PI0735|3end_ABC_transporter,_ATP-binding_/_permease_670591..670741_POSITIVE 149 87 46 118 76 pint:PI0069|3end_hypothetical_protein_67379..67529_POSITIVE 149 90 47 48 9 pint:PI0024|3end_hypothetical_protein_28559..28709_POSITIVE 148 77 38 118 87 pint:PI2140|3end_conserved_hypothetical_protein_2087167..2087317_POSITIVE 148 105 76 108 74 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 145 105 77 68 39 pint:PI1184|3end_conserved_hypothetical_protein_1106163..1106313_POSITIVE 145 89 64 39 12 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE