Origin IGS: tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa .........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 ttgataggggtgatataggcgacttcgacttgaaagagtcttatctcggattgacttcatcacaacagcacgaggccaaaacatgctaaagaacattttcccgacaaaaaagacgtaaacgatcgaaaaaaccgtctttataggtatcaggagggaaagaatacctatctttgaggcgtcaagattactcacttttaggtattcgaagtccttattaaaaagataactata Mask Tandem Repeat Region ================================================ tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa Find is-nt database================================================ Query_seq: PG1813:PG1814|PG1813:PG1814:ferredoxin, 4Fe-4S:DNA primase:<-<-:1908465..1908695 231 tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1813:PG1814|PG1813:PG1814:ferredoxin, 4Fe-4S:DNA primase:<-<-:1908465..1908695 231 tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1813:PG1814|PG1813:PG1814:ferredoxin, 4Fe-4S:DNA primase:<-<-:1908465..1908695 231 tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 40 End: 231 ....................................... M S N L D A S K I G I L S L L I P I K T V F S I V Y V F F V G K M F F S M F W P R A V V M K S I R D K T L S S R S R L Y Protein_Len: 34 Strand: - Start: 9 End: 110 ........ R K L L S K S Y R F T L L R S A E F I P I R E R R I G I F V T K E M ......................................................................................................................... tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa 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================================================ tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1813:PG1814|PG1813:PG1814:ferredoxin, 4Fe-4S:DNA primase:<-<-:1908465..1908695 231 tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa Intra-Species Hit: Count: 1 Min: 1 Max: 231 Len: 231 Subject: NC_002950_PG1813_PG1814|ferredoxin, 4Fe-4S:DNA primase|NEGATIVE:NEGATIVE|[1908465,1908695]|231 HSP 1 e-value: 1.0E-128 bit: 458.0 Len: 231 Query Start:1 Query End:231 Subject Strand: POSITIVE Subject Start: 1 Subject End: 231 tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa tatagttatctttttaataaggacttcgaatacctaaaagtgagtaatcttgacgcctcaaagataggtattctttccctcctgatacctataaagacggttttttcgatcgtttacgtcttttttgtcgggaaaatgttctttagcatgttttggcctcgtgctgttgtgatgaagtcaatccgagataagactctttcaagtcgaagtcgcctatatcacccctatcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAGUUAUCUUUUUAAUAAGGACUUCGAAUACCUAAAAGUGAGUAAUCUUGACGCCUCAAAGAUAGGUAUUCUUUCCCUCCUGAUACCUAUAAAGACGGUUUUUUCGAUCGUUUACGUCUUUUUUGUCGGGAAAAUGUUCUUUAGCAUGUUUUGGCCUCGUGCUGUUGUGAUGAAGUCAAUCCGAGAUAAGACUCUUUCAAGUCGAAGUCGCCUAUAUCACCCCUAUCAA (((((.((((((.........(((((((((((((((....((((............))))....)))))))))......((((((((.....(((((((.................)))))))..)))))))).......(..(((((((.........)))))))..)....)))))).....)))))).((((......))))........)))))............. (-51.87) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAUAGGGGUGAUAUAGGCGACUUCGACUUGAAAGAGUCUUAUCUCGGAUUGACUUCAUCACAACAGCACGAGGCCAAAACAUGCUAAAGAACAUUUUCCCGACAAAAAAGACGUAAACGAUCGAAAAAACCGUCUUUAUAGGUAUCAGGAGGGAAAGAAUACCUAUCUUUGAGGCGUCAAGAUUACUCACUUUUAGGUAUUCGAAGUCCUUAUUAAAAAGAUAACUAUA (((((((((........(((......(((((....)))))....((((..(((............)))..))))))).......(((.........((((((..(......((((....)).))......(((.........)))....)..))))))(((((((((....((((..((....))..))))....)))))))))..))))))))))))............. (-53.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 926 100 51 191 142 NC_002950:PG1813|5end_ferredoxin,_4Fe-4S_1908374..1908604_NEGATIVE 331 178 137 151 106 NC_002950:PG0445|5end_peptidase_T_485252..485482_POSITIVE 325 193 152 157 114 NC_002950:PG1511|5end_hypothetical_protein_1587609..1587839_POSITIVE 324 214 177 222 183 NC_002950:PG1604|5end_immunoreactive_84_kDa_antigen_PG93_1682737..1682967_POSITIVE 321 180 140 45 6 NC_002950:PG0232|5end_zinc_carboxypeptidase,_putative_269923..270153_NEGATIVE 319 189 148 179 136 NC_002950:PG0756|5end_hypothetical_protein_805673..805903_NEGATIVE 314 168 124 210 156 NC_002950:PG0740|5end_NLP/P60_family_protein_787836..788066_POSITIVE 312 179 136 172 130 NC_002950:PG2069|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2164798..2165028_POSITIVE 310 130 81 65 10 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 309 185 142 159 108 NC_002950:PG1664|5end_ABC_transporter,_permease_protein,_putative_1745813..1746043_POSITIVE 309 213 172 82 30 NC_002950:PG1066|5end_butyrate-acetoacetate_CoA-transferase,_subunit_A_1133521..1133751_POSITIVE 305 137 93 57 4 NC_002950:PG1596|5end_isoleucyl-tRNA_synthetase,_putative_1674543..1674773_POSITIVE 302 160 111 99 54 NC_002950:PG2071|5end_hypothetical_protein_2166437..2166667_POSITIVE 302 206 161 182 140 NC_002950:PG0134|5end_magnesium_transporter_157135..157365_NEGATIVE 298 209 163 214 165 NC_002950:PG2076|5end_hypothetical_protein_2176445..2176675_POSITIVE 298 175 145 145 119 NC_002950:PG1359|5end_hypothetical_protein_1438615..1438845_NEGATIVE 298 209 163 214 165 NC_002950:PG1267|5end_hypothetical_protein_1346966..1347196_POSITIVE 296 159 111 73 30 NC_002950:PG0022|5end_sulfate_permease_family_protein_26796..27026_NEGATIVE 292 193 152 128 80 NC_002950:PG1221|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1298129..1298359_POSITIVE 292 120 73 100 60 NC_002950:PG1167|5end_hypothetical_protein_1248427..1248657_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 158 111 78 16 NC_002950:PG2172|3end_hypothetical_protein_2279191..2279341_NEGATIVE 331 178 137 134 89 NC_002950:PG0444|3end_oligopeptide_transporter,_OPT_family_485315..485465_POSITIVE 319 189 148 129 86 NC_002950:PG0757|3end_hypothetical_protein_805723..805873_NEGATIVE 309 185 142 134 83 NC_002950:PG1663|3end_ABC_transporter,_ATP-binding_protein_1745868..1746018_POSITIVE 304 185 141 127 88 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 302 160 111 129 84 NC_002950:PG2070|3end_hypothetical_protein_2166547..2166697_POSITIVE 302 206 161 150 108 NC_002950:PG0135|3end_dimethyladenosine_transferase_157167..157317_NEGATIVE 298 175 145 142 116 NC_002950:PG1360|3end_phosphoribosylamine--glycine_ligase_1438618..1438768_NEGATIVE 294 133 95 71 38 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 292 193 152 118 70 NC_002950:PG1220|3end_erythronate-4-phosphate_dehydrogenase_1298199..1298349_POSITIVE 290 173 131 141 96 NC_002950:PG1458|3end_hypothetical_protein_1539682..1539832_POSITIVE 287 188 145 142 105 NC_002950:PG1960|3end_ribosomal_protein_L28_2048424..2048574_NEGATIVE 286 185 146 133 84 NC_002950:PG2152|3end_DNA-binding_protein,_histone-like_family_2260315..2260465_POSITIVE 286 199 152 53 1 NC_002950:PG1722|3end_hypothetical_protein_1812633..1812783_NEGATIVE 285 89 49 138 94 NC_002950:PG0633|3end_hypothetical_protein_686208..686358_POSITIVE 284 177 131 111 59 NC_002950:PG0055|3end_hypothetical_protein_67951..68101_POSITIVE 283 150 110 142 103 NC_002950:PG0615|3end_GTP-binding_protein_TypA_668912..669062_POSITIVE 282 193 153 74 33 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 280 186 142 140 98 NC_002950:PG1279|3end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_1357535..1357685_POSITIVE 275 188 147 141 100 NC_002950:PG1881|3end_hypothetical_protein_1978046..1978196_POSITIVE