Origin IGS: tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttctgatttaatttaagttccacaaaatagttgttatttaaatgtattttctttataaatgaggtatgtttcttttagttttatgacacgtgttgccatttatcgtatcta Mask Tandem Repeat Region ================================================ tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag Find is-nt database================================================ Query_seq: PI0022:PI0023|PI0022:PI0023:hypothetical protein:internalin-related protein:->->:25952..26063 112 tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0022:PI0023|PI0022:PI0023:hypothetical protein:internalin-related protein:->->:25952..26063 112 tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0022:PI0023|PI0022:PI0023:hypothetical protein:internalin-related protein:->->:25952..26063 112 tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag Predict ORF larger than 30AA ================================================ tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag 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: 53 End: 82 ....................................................GTTGTTATTTAAATGTATTTTCTTTATAAA.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0022:PI0023|PI0022:PI0023:hypothetical protein:internalin-related protein:->->:25952..26063 112 tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: pint_PI0022_PI0023|hypothetical protein:internalin-related protein|POSITIVE:POSITIVE|[25952,26063]|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 tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag tagatacgataaatggcaacacgtgtcataaaactaaaagaaacatacctcatttataaagaaaatacatttaaataacaactattttgtggaacttaaattaaatcagaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUACGAUAAAUGGCAACACGUGUCAUAAAACUAAAAGAAACAUACCUCAUUUAUAAAGAAAAUACAUUUAAAUAACAACUAUUUUGUGGAACUUAAAUUAAAUCAGAAG ..((((((.....((....)))))))).....................((.(((((..(((....((((...(((((.....)))))))))...)))....))))).))... (-11.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUGAUUUAAUUUAAGUUCCACAAAAUAGUUGUUAUUUAAAUGUAUUUUCUUUAUAAAUGAGGUAUGUUUCUUUUAGUUUUAUGACACGUGUUGCCAUUUAUCGUAUCUA ...........((((((((..(((......).))..))))))))...........(((((((.(((((((.((............)).)))))))..)))))))........ (-11.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 50 3 122 61 pint:PI0977|5end_riboflavin_synthase,_alpha_subunit_904043..904273_POSITIVE 201 50 3 125 85 pint:PI0493|5end_surface_antigen_BspA_452844..453074_POSITIVE 193 28 2 126 100 pint:PI0806|5end_heavy_metal_efflux_pump_743679..743909_POSITIVE 191 28 6 23 3 pint:PI1068|5end_nucleolar_protein,_Sun_(Fmu)_family_protein;_tRNA/rRNA_cytosine-C5-methylase_984743..984973_POSITIVE 187 29 5 179 152 pint:PI0802|5end_hypothetical_protein_739544..739774_POSITIVE 183 34 1 114 81 pint:PI1932|5end_glycogen_synthase_1878080..1878310_POSITIVE 183 48 8 129 89 pint:PI0555|5end_conserved_hypothetical_protein_504577..504807_POSITIVE 182 24 9 162 147 pint:PI0581|5end_conserved_hypothetical_protein_525055..525285_POSITIVE 181 35 7 83 52 pint:PI0488|5end_conserved_hypothetical_protein_446906..447136_POSITIVE 180 49 14 183 139 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 173 49 2 143 94 pint:PI2040|5end_conserved_hypothetical_protein;_possible_transporter_1993068..1993298_POSITIVE 173 29 1 201 168 pint:PI0126|5end_conserved_hypothetical_protein_117925..118155_POSITIVE 172 43 7 71 38 pint:PI0455|5end_hypothetical_protein_427361..427591_POSITIVE 171 43 5 124 83 pint:PI0060|5end_long-chain-fatty-acid--CoA_ligase_(acyl-CoA_synthetase)_58281..58511_POSITIVE 170 49 2 82 44 pint:PI0824|5end_large_conductance_mechanosensitive_channel_protein_763337..763567_POSITIVE 169 24 3 72 53 pint:PI1890|5end_cell_division_protein_FtsW_1832886..1833116_POSITIVE 167 53 16 220 191 pint:PI0131|5end_conserved_hypothetical_protein_(possible_outer_membrane_lipoprotein)_122490..122720_POSITIVE 165 30 5 211 187 pint:PI0597|5end_hypothetical_protein_546626..546856_POSITIVE 164 55 15 111 70 pint:PI0259|5end_conserved_protein_found_in_conjugation,_TraI_252355..252585_POSITIVE 163 27 1 36 12 pint:PI1975|5end_conserved_hypothetical_protein_1931513..1931743_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 198 38 7 105 78 pint:PI1547|3end_hypothetical_protein_1466226..1466376_POSITIVE 183 34 1 45 12 pint:PI1931|3end_alpha_glycan_phosphorylase,_maltodextrin_phosphorylase_1878091..1878241_POSITIVE 183 48 8 71 31 pint:PI0554|3end_hypothetical_protein_504599..504749_POSITIVE 173 29 1 86 53 pint:PI0125|3end_undecaprenyl_pyrophosphate_synthase_117890..118040_POSITIVE 165 30 5 113 89 pint:PI0596|3end_hypothetical_protein_546608..546758_POSITIVE 163 27 1 30 6 pint:PI1974|3end_hypothetical_protein_1931587..1931737_POSITIVE 163 50 14 87 56 pint:PI0432|3end_hypothetical_protein_405037..405187_POSITIVE 163 50 14 123 92 pint:PI0433|3end_hypothetical_protein_405073..405223_POSITIVE 162 49 4 129 92 pint:PI0113|3end_arginyl-tRNA_synthetase_110082..110232_POSITIVE 161 31 4 34 1 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 159 54 23 46 7 pint:PI1110|3end_probable_glycosyltransferase,_family_8_1034783..1034933_POSITIVE 159 29 12 106 90 pint:PI0765|3end_conserved_hypothetical_protein;_possible_surface_protein_700822..700972_POSITIVE 154 28 8 31 13 pint:PI1545|3end_conserved_hypothetical_protein_1464134..1464284_POSITIVE 153 47 1 147 102 pint:PI0918|3end_Fe-S_oxidoreductase,_family_2_849236..849386_POSITIVE 152 50 6 139 98 pint:PI1741|3end_lipid-A-disaccharide_synthase_1663856..1664006_POSITIVE 150 43 15 82 46 pint:PI2140|3end_conserved_hypothetical_protein_2087167..2087317_POSITIVE 150 47 3 46 1 pint:PI1467|3end_conserved_hypothetical_protein_1393909..1394059_POSITIVE 148 48 2 82 23 pint:PI1806|3end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1742191..1742341_POSITIVE 148 27 2 139 116 pint:PI1271|3end_transcriptional_regulator,__AraC/XylS_family_1191284..1191434_POSITIVE 148 65 28 46 2 pint:PI0129|3end_hypothetical_protein_121941..122091_POSITIVE