Origin IGS: gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt .........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 actgaaccatagacccagaaaaaactaaactttagaactcctttcgagtgcttcttgctaaatttatcttagtgttgcatttgtttgtgggatgtgtacctcaaatcgtttaggagactattgaagaaaaaggattattttcgcgaggtaaaatgtaggaatacaataagattcacacatcaagatagc Mask Tandem Repeat Region ================================================ gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt Find is-nt database================================================ Query_seq: PG2165:PG2166|PG2165:PG2166:glycyl-tRNA synthetase:hypothetical protein:<-->:2271760..2271948 189 gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2165:PG2166|PG2165:PG2166:glycyl-tRNA synthetase:hypothetical protein:<-->:2271760..2271948 189 gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2165:PG2166|PG2165:PG2166:glycyl-tRNA synthetase:hypothetical protein:<-->:2271760..2271948 189 gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 1 End: 111 S D Q H T F R I T N R C K V E R F Y D K K K L L R R F S K L Y V D W L C M .............................................................................. gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt 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================================================ gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -4.0 Tail_Score: -5.29782 Start: 155 End: 165 Full_Region: CACTCGAAAGGAGTT CTAA AGT TTAG TTTTTTCTGGGTCTA ..........................................................................................................................................................CTAAAGTTTAG........................ Find igs database================================================ Query_seq: PG2165:PG2166|PG2165:PG2166:glycyl-tRNA synthetase:hypothetical protein:<-->:2271760..2271948 189 gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: NC_002950_PG2165_PG2166|glycyl-tRNA synthetase:hypothetical protein|NEGATIVE:POSITIVE|[2271760,2271948]|189 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 189 gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt gctatcttgatgtgtgaatcttattgtattcctacattttacctcgcgaaaataatcctttttcttcaatagtctcctaaacgatttgaggtacacatcccacaaacaaatgcaacactaagataaatttagcaagaagcactcgaaaggagttctaaagtttagttttttctgggtctatggttcagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUAUCUUGAUGUGUGAAUCUUAUUGUAUUCCUACAUUUUACCUCGCGAAAAUAAUCCUUUUUCUUCAAUAGUCUCCUAAACGAUUUGAGGUACACAUCCCACAAACAAAUGCAACACUAAGAUAAAUUUAGCAAGAAGCACUCGAAAGGAGUUCUAAAGUUUAGUUUUUUCUGGGUCUAUGGUUCAGU (((.(((((....((..((((((.(((............((((((..(((((.......)))))......((((........)))).)))))).........((......))..))).))))))..))....))))))))..((....)).(..(((.(((((((......))))).)).)))..)... (-31.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGAACCAUAGACCCAGAAAAAACUAAACUUUAGAACUCCUUUCGAGUGCUUCUUGCUAAAUUUAUCUUAGUGUUGCAUUUGUUUGUGGGAUGUGUACCUCAAAUCGUUUAGGAGACUAUUGAAGAAAAAGGAUUAUUUUCGCGAGGUAAAAUGUAGGAAUACAAUAAGAUUCACACAUCAAGAUAGC ......((((((((..........(((.....)))..........((((((....((((((.......))))))..))))))))))))))((((((((((((...(((..(((....))).))).(((((.......)))))..)))))....((((....)))).........)))))))........ (-40.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 873 120 71 211 162 NC_002950:PG2165|5end_glycyl-tRNA_synthetase_2271669..2271899_NEGATIVE 492 156 111 228 183 NC_002950:PG1707|5end_hypothetical_protein_1794597..1794827_NEGATIVE 372 150 108 219 178 NC_002950:PG1215|5end_lipoprotein_protein,_putative_1294621..1294851_POSITIVE 307 156 122 185 145 NC_002950:PG1559|5end_aminomethyltransferase_1638992..1639222_NEGATIVE 290 179 139 61 18 NC_002950:PG0923|5end_ribosome-binding_factor_A_982814..983044_NEGATIVE 276 100 56 178 122 NC_002950:PG1394|5end_hypothetical_protein_1476782..1477012_NEGATIVE 275 88 44 170 129 NC_002950:PG1961|5end_hypothetical_protein_2051153..2051383_NEGATIVE 272 141 111 230 200 NC_002950:PG2085|5end_tryptophanyl-tRNA_synthetase_2185532..2185762_POSITIVE 270 100 56 80 38 NC_002950:PG0464|5end_adenylosuccinate_synthetase_508874..509104_NEGATIVE 264 179 131 69 14 NC_002950:PG0785|5end_tonB_protein,_putative_837592..837822_NEGATIVE 261 180 148 30 3 NC_002950:PG1753|5end_selenide,_water_dikinase_1838615..1838845_POSITIVE 258 105 61 154 110 NC_002950:PG0614|5end_hypothetical_protein_665847..666077_POSITIVE 256 83 43 71 37 NC_002950:PG0571|5end_aspartate-semialdehyde_dehydrogenase_626399..626629_POSITIVE 252 84 43 159 119 NC_002950:PG1221|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1298129..1298359_POSITIVE 246 176 132 171 115 NC_002950:PG1516|5end_hypothetical_protein_1591741..1591971_POSITIVE 244 98 58 172 129 NC_002950:PG0003|5end_hypothetical_protein_2938..3168_NEGATIVE 234 46 12 59 26 NC_002950:PG0384|5end_MutS2_family_protein_416095..416325_POSITIVE 233 178 131 58 14 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 232 100 56 224 170 NC_002950:PG1423|5end_hypothetical_protein_1509088..1509318_NEGATIVE 231 175 131 93 47 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 156 122 110 70 NC_002950:PG1560|3end_dTDP-glucose_4,6-dehydratase_1639067..1639217_NEGATIVE 285 179 131 53 8 NC_002950:PG0568|3end_elongation_factor_P_623999..624149_NEGATIVE 270 100 56 51 9 NC_002950:PG0465|3end_ferric_uptake_transcriptional_regulator_508903..509053_NEGATIVE 264 180 144 33 1 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 264 179 131 91 36 NC_002950:PG0786|3end_hypothetical_protein_837570..837720_NEGATIVE 256 90 41 74 23 NC_002950:PG1038|3end_ATP-dependent_DNA_helicase_UvrD/PcrA/Rep_Family_1105121..1105271_POSITIVE 252 84 43 149 109 NC_002950:PG1220|3end_erythronate-4-phosphate_dehydrogenase_1298199..1298349_POSITIVE 248 179 138 89 48 NC_002950:PG1667|3end_outer_membrane_efflux_protein_1750992..1751142_POSITIVE 247 101 62 70 32 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 242 100 71 145 107 NC_002950:PG0492|3end_hypothetical_protein_534408..534558_NEGATIVE 241 176 131 44 8 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 241 77 31 59 19 NC_002950:PG0545|3end_hypothetical_protein_600228..600378_POSITIVE 236 177 135 52 7 NC_002950:PG0571|3end_aspartate-semialdehyde_dehydrogenase_627492..627642_POSITIVE 234 46 12 49 16 NC_002950:PG0383|3end_membrane-associated_zinc_metalloprotease,_putative_416165..416315_POSITIVE 231 175 131 96 50 NC_002950:PG1380|3end_ABC_transporter,_ATP-binding_protein_1460705..1460855_POSITIVE 230 88 56 39 6 NC_002950:PG1136|3end_hypothetical_protein_1216699..1216849_NEGATIVE 229 176 131 111 69 NC_002950:PG1831|3end_ATP-dependent_DNA_helicase_RecQ_1923455..1923605_NEGATIVE 221 116 75 69 21 NC_002950:PG2216|3end_hypothetical_protein_2329530..2329680_POSITIVE 220 153 117 58 13 NC_002950:PG0468|3end_mannose-6-phosphate_isomerase,_class_I_510374..510524_NEGATIVE 218 112 72 130 86 NC_002950:PG1954|3end_NAD_dependent_epimerase/reductase-related_protein_2045612..2045762_POSITIVE