Origin IGS: aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actcgtcttcgttgttgaaaacttttttggcgcatgatttttgagtgagtaattgtatttacagctacccttttgtggtctctttgaattttcgaaggtgttt Mask Tandem Repeat Region ================================================ aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt Find is-nt database================================================ Query_seq: PG0608:PG0609|PG0608:PG0609:hypothetical protein:hypothetical protein:->->:663220..663322 103 aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0608:PG0609|PG0608:PG0609:hypothetical protein:hypothetical protein:->->:663220..663322 103 aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0608:PG0609|PG0608:PG0609:hypothetical protein:hypothetical protein:->->:663220..663322 103 aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt Predict ORF larger than 30AA ================================================ aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt 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================================================ aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0608:PG0609|PG0608:PG0609:hypothetical protein:hypothetical protein:->->:663220..663322 103 aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002950_PG0608_PG0609|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[663220,663322]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt aaacaccttcgaaaattcaaagagaccacaaaagggtagctgtaaatacaattactcactcaaaaatcatgcgccaaaaaagttttcaacaacgaagacgagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACACCUUCGAAAAUUCAAAGAGACCACAAAAGGGUAGCUGUAAAUACAAUUACUCACUCAAAAAUCAUGCGCCAAAAAAGUUUUCAACAACGAAGACGAGU ......(((.((....)).)))...........((((((.(((....))).))))))........................((((((......)))))).... (-12.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCGUCUUCGUUGUUGAAAACUUUUUUGGCGCAUGAUUUUUGAGUGAGUAAUUGUAUUUACAGCUACCCUUUUGUGGUCUCUUUGAAUUUUCGAAGGUGUUU (((((...(((((((..(((....)))..))).))))....)))))..((((......)))).(((((......))))).(((((((....)))))))..... (-20.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 470 100 58 179 140 NC_002950:PG1148|5end_hypothetical_protein_1231204..1231434_POSITIVE 470 100 55 210 166 NC_002950:PG0996|5end_conserved_hypothetical_protein_TIGR01777_1055592..1055822_POSITIVE 403 100 67 215 184 NC_002950:PG1166|5end_hypothetical_protein_1248443..1248673_NEGATIVE 315 98 59 48 10 NC_002950:PG1573|5end_transcriptional_regulator,_Crp_family_1652168..1652398_NEGATIVE 241 50 10 84 43 NC_002950:PG0610|5end_hypothetical_protein_664023..664253_NEGATIVE 236 61 26 45 4 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 226 44 3 182 138 NC_002950:PG0952|5end_4-hydroxy-3-methylbut-2-en-1-yl_diphosphate_synthase_1010922..1011152_POSITIVE 225 41 7 64 28 NC_002950:PG1706|5end_hypothetical_protein_1794211..1794441_NEGATIVE 225 44 4 104 70 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 211 42 7 165 124 NC_002950:PG1524|5end_2-succinyl-6-hydroxy-2,_4-cyclohexadiene-1-carboxylic_acid_synthase/2-oxoglutarate_decarboxylase_1602746..1602976_NEGATIVE 209 40 3 196 153 NC_002950:PG1829|5end_long-chain-fatty-acid--CoA_ligase,_putative_1922980..1923210_NEGATIVE 208 100 52 152 84 NC_002950:PG0142|5end_SpoOJ_regulator_protein_165531..165761_NEGATIVE 207 61 25 45 5 NC_002950:PG1779|5end_hypothetical_protein_1867924..1868154_POSITIVE 207 50 4 197 144 NC_002950:PG0450|5end_hypothetical_protein_490812..491042_POSITIVE 203 69 21 87 42 NC_002950:PG2168|5end_hypothetical_protein_2274157..2274387_NEGATIVE 203 75 31 199 155 NC_002950:PG1921|5end_ribosomal_protein_S5_2017021..2017251_NEGATIVE 201 98 70 108 84 NC_002950:PG0504|5end_lipoyl_synthase_544234..544464_POSITIVE 201 42 9 159 126 NC_002950:PG0498|5end_S-ribosylhomocysteinase_537968..538198_POSITIVE 199 100 51 65 9 NC_002950:PG2167|5end_immunoreactive_53_kDa_antigen_PG123_2273543..2273773_NEGATIVE 199 44 4 139 97 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 60 20 99 65 NC_002950:PG1761|3end_acetyltransferase,_GNAT_family_1847739..1847889_POSITIVE 225 41 7 43 7 NC_002950:PG1707|3end_hypothetical_protein_1794232..1794382_NEGATIVE 210 46 21 22 1 NC_002950:PG2077|3end_hypothetical_protein_2177005..2177155_NEGATIVE 203 95 69 76 52 NC_002950:PG2166|3end_hypothetical_protein_2271999..2272149_POSITIVE 201 42 9 134 101 NC_002950:PG0497|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase_538023..538173_POSITIVE 196 99 66 54 17 NC_002950:PG1416|3end_enoyl-(acyl-carrier-protein)_reductase_II_1501078..1501228_POSITIVE 190 96 55 104 61 NC_002950:PG0287|3end_hypothetical_protein_321478..321628_POSITIVE 186 44 10 59 18 NC_002950:PG1786|3end_hypothetical_protein_1875322..1875472_POSITIVE 186 46 6 54 22 NC_002950:PG1580|3end_hypothetical_protein_1658451..1658601_POSITIVE 186 79 32 67 3 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 184 42 4 72 33 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 183 75 34 129 75 NC_002950:PG0660|3end_nitroreductase_family_protein_709141..709291_NEGATIVE 183 87 61 44 11 NC_002950:PG0542|3end_hypothetical_protein_595377..595527_NEGATIVE 183 80 32 87 46 NC_002950:PG0422|3end_hypothetical_protein_461931..462081_NEGATIVE 183 100 65 149 115 NC_002950:PG0356|3end_hypothetical_protein_391473..391623_POSITIVE 181 43 6 39 5 NC_002950:PG0409|3end_hypothetical_protein_442350..442500_POSITIVE 180 40 18 138 117 NC_002950:PG1897|3end_thiamin_pyrophosphokinase_catalytic_domain_protein_1996053..1996203_NEGATIVE 179 42 4 56 20 NC_002950:PG2050|3end_hypothetical_protein_2149159..2149309_NEGATIVE 176 44 7 63 28 NC_002950:PG1508|3end_hypothetical_protein_1586688..1586838_POSITIVE 176 42 7 84 56 NC_002950:PG0532|3end_hypothetical_protein_581249..581399_NEGATIVE