Origin IGS: agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacaatgcaactgtaaaataatatccatatatttgtaactataaaatattaacaaaaactttattcattatgaaaagaaaaggaattaaaacggcaatatgccttatggcaggcact Mask Tandem Repeat Region ================================================ agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta Find is-nt database================================================ Query_seq: PI0294:PI0295|PI0294:PI0295:conserved hypothetical protein:lysine decarboxylase:->->:276867..276985 119 agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0294:PI0295|PI0294:PI0295:conserved hypothetical protein:lysine decarboxylase:->->:276867..276985 119 agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0294:PI0295|PI0294:PI0295:conserved hypothetical protein:lysine decarboxylase:->->:276867..276985 119 agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta Predict ORF larger than 30AA ================================================ agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta 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: 43 End: 72 ..........................................TTTCATAATGAATAAAGTTTTTGTTAATAT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0294:PI0295|PI0294:PI0295:conserved hypothetical protein:lysine decarboxylase:->->:276867..276985 119 agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: pint_PI0294_PI0295|conserved hypothetical protein:lysine decarboxylase|POSITIVE:POSITIVE|[276867,276985]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta agtgcctgccataaggcatattgccgttttaattccttttcttttcataatgaataaagtttttgttaatattttatagttacaaatatatggatattattttacagttgcattgttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGCCUGCCAUAAGGCAUAUUGCCGUUUUAAUUCCUUUUCUUUUCAUAAUGAAUAAAGUUUUUGUUAAUAUUUUAUAGUUACAAAUAUAUGGAUAUUAUUUUACAGUUGCAUUGUUUA .((((((......))))))...............................(((((((.((..((((((((((((((((........)))).))))))))....))))..)).))))))) (-19.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAAUGCAACUGUAAAAUAAUAUCCAUAUAUUUGUAACUAUAAAAUAUUAACAAAAACUUUAUUCAUUAUGAAAAGAAAAGGAAUUAAAACGGCAAUAUGCCUUAUGGCAGGCACU .......(((..((((....((((.(((.....(((((...............)))))..((((..((.....))))))....)))))))..)))).....((((....)))).))).. (-14.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 48 1 98 48 pint:PI0747|5end_possible_mobilization_protein_676326..676556_POSITIVE 305 48 3 109 58 pint:PI0259|5end_conserved_protein_found_in_conjugation,_TraI_252355..252585_POSITIVE 288 44 1 63 26 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 278 43 5 184 149 pint:PI1230|5end_probable_metallo-beta-lactamase_family_protein_1151840..1152070_POSITIVE 267 50 2 60 1 pint:PI0571|5end_conserved_hypothetical_protein;_possible_permease_515161..515391_POSITIVE 258 38 2 71 31 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 252 27 2 209 184 pint:PI0817|5end_glycosyl_transferase,_group_1_family_protein_756861..757091_POSITIVE 247 48 6 81 39 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 247 46 1 58 8 pint:PI0010|5end_conserved_hypothetical_protein_10628..10858_POSITIVE 244 54 12 158 110 pint:PI0518|5end_5'-nucleotidase_precursor_477076..477306_POSITIVE 240 49 2 92 34 pint:PI1771|5end_alpha-glucosidase_1699996..1700226_POSITIVE 240 45 4 113 72 pint:PI0499|5end_integrase,_C-terminal_region_460237..460467_POSITIVE 237 43 3 135 95 pint:PI1863|5end_phosphoribosylformylglycinamidine_synthase_1806674..1806904_POSITIVE 236 45 4 127 94 pint:PI1363|5end_hypothetical_protein_1281666..1281896_POSITIVE 234 47 2 205 157 pint:PI1383|5end_biopolymer_transport_protein_tolQ_related_1304121..1304351_POSITIVE 229 38 3 120 80 pint:PI1854|5end_possible_glycosyl_transferase_1800925..1801155_POSITIVE 229 48 1 163 115 pint:PI0984|5end_hypothetical_protein_909936..910166_POSITIVE 224 30 1 177 146 pint:PI0960|5end_hypothetical_protein_891137..891367_POSITIVE 222 35 1 116 76 pint:PI2105|5end_hypothetical_protein_2059357..2059587_POSITIVE 222 25 5 212 193 pint:PI1452|5end_possible_nicotinamide_mononucleotide_transporter_1375353..1375583_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 48 1 111 61 pint:PI0746|3end_hypothetical_protein_676419..676569_POSITIVE 288 44 1 60 23 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 287 47 3 145 103 pint:PI1981|3end_hypothetical_protein_1938138..1938288_POSITIVE 259 41 4 68 27 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 247 48 6 68 26 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 244 54 12 86 38 pint:PI0517|3end_apparent_PorT_homolog_477084..477234_POSITIVE 242 43 3 147 114 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 240 45 4 135 94 pint:PI0498|3end_integrase_460339..460489_POSITIVE 236 29 2 36 11 pint:PI2036|3end_hypothetical_protein_1989516..1989666_POSITIVE 234 47 2 141 93 pint:PI1382|3end_hypothetical_protein_1304137..1304287_POSITIVE 232 36 1 147 103 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 229 48 1 138 90 pint:PI0983|3end_hypothetical_protein_909991..910141_POSITIVE 222 35 1 69 29 pint:PI2104|3end_carboxyl-terminal_protease_2059390..2059540_POSITIVE 222 25 5 144 125 pint:PI1451|3end_outer_membrane_receptor_proteins,_tonB_dependent_(possibly_iron_transport_related)_1375365..1375515_POSITIVE 218 26 2 151 126 pint:PI2078|3end_hypothetical_protein_2036783..2036933_POSITIVE 218 47 3 55 7 pint:PI0011|3end_conserved_hypothetical_protein_13328..13478_POSITIVE 217 30 1 72 38 pint:PI1927|3end_hypothetical_protein_1872046..1872196_POSITIVE 216 47 10 70 35 pint:PI0731|3end_conserved_hypothetical_protein_663673..663823_POSITIVE 214 43 3 88 39 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 212 41 1 45 3 pint:PI1686|3end_hypothetical_protein_1601898..1602048_POSITIVE