Origin IGS: tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acctagaatattttctaggttttttaattgatttgaatgttaatgaatgtcttttcgcaaacttaacaaaatatgatataatgaagtgctactaaaaaaggtttcattagccttgaaaggattaaaaa Mask Tandem Repeat Region ================================================ tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt Find is-nt database================================================ Query_seq: SSA_1703:SSA_1704|SSA_1703:SSA_1704:Methionyl-tRNA synthetase, putative:Conserved uncharacterized protein:<-<-:1695731..1695858 128 tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1703:SSA_1704|SSA_1703:SSA_1704:Methionyl-tRNA synthetase, putative:Conserved uncharacterized protein:<-<-:1695731..1695858 128 tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1703:SSA_1704|SSA_1703:SSA_1704:Methionyl-tRNA synthetase, putative:Conserved uncharacterized protein:<-<-:1695731..1695858 128 tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt Predict ORF larger than 30AA ================================================ tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt 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: 84 Start: 47 End: 76 ..............................................TTTCGCAAACTTAACAAAATATGATATAAT.................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1703:SSA_1704|SSA_1703:SSA_1704:Methionyl-tRNA synthetase, putative:Conserved uncharacterized protein:<-<-:1695731..1695858 128 tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_009009_SSA_1703_SSA_1704|Methionyl-tRNA synthetase, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[1695731,1695858]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt tttttaatcctttcaaggctaatgaaaccttttttagtagcacttcattatatcatattttgttaagtttgcgaaaagacattcattaacattcaaatcaattaaaaaacctagaaaatattctaggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAAUCCUUUCAAGGCUAAUGAAACCUUUUUUAGUAGCACUUCAUUAUAUCAUAUUUUGUUAAGUUUGCGAAAAGACAUUCAUUAACAUUCAAAUCAAUUAAAAAACCUAGAAAAUAUUCUAGGU .(((((((......(((((((.(((((....))))).)))).)))...............(((((((..(((.....).))..).)))))).........))))))).((((((((....)))))))) (-20.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUAGAAUAUUUUCUAGGUUUUUUAAUUGAUUUGAAUGUUAAUGAAUGUCUUUUCGCAAACUUAACAAAAUAUGAUAUAAUGAAGUGCUACUAAAAAAGGUUUCAUUAGCCUUGAAAGGAUUAAAAA ((((((((....)))))))).((((((((..(((.((.(((((((((...(((((.....((((...................))))........)))))..))))))))).)).))).)))))))). (-25.13) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 734 50 1 141 92 NC_009009:SSA_1703|5end_Methionyl-tRNA_synthetase,_putative_1695640..1695870_NEGATIVE 267 47 5 122 83 NC_009009:SSA_1557|5end_SRPR,_signal_recognition_particle-docking_protein,_putative_1560040..1560270_NEGATIVE 262 75 38 145 108 NC_009009:SSA_1283|5end_Nitroreductase,_putative_1304336..1304566_NEGATIVE 254 80 34 158 111 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 240 47 8 192 144 NC_009009:SSA_1199|5end_Phosphinothricin_acetyltransferase,_putative_1223958..1224188_NEGATIVE 222 50 10 59 13 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 217 46 8 87 52 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 211 46 6 61 16 NC_009009:SSA_1471|5end_hypothetical_protein_1478144..1478374_NEGATIVE 204 82 52 172 135 NC_009009:SSA_0746|5end_Glucosamine-6-phosphate_deaminase,_putative_727078..727308_POSITIVE 203 78 36 68 21 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 201 72 35 182 143 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 200 73 31 180 140 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 200 64 22 142 90 NC_009009:SSA_0384|5end_hypothetical_protein_376240..376470_POSITIVE 199 60 13 134 91 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 198 50 13 38 7 NC_009009:SSA_1494|5end_Conserved_uncharacterized_protein_1500773..1501003_NEGATIVE 198 55 16 231 192 NC_009009:SSA_1315|5end_hypothetical_protein_1332052..1332282_NEGATIVE 198 79 35 187 137 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 197 48 1 107 46 NC_009009:SSA_1995|5end_hypothetical_protein_1993358..1993588_NEGATIVE 197 25 8 75 56 NC_009009:SSA_0739|5end_Carbamate_kinase,_putative_721087..721317_POSITIVE 197 46 10 155 118 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 47 5 118 79 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 254 80 34 62 15 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 250 85 43 43 1 NC_009009:SSA_1284|3end_hypothetical_protein_1304446..1304596_NEGATIVE 211 50 2 80 22 NC_009009:SSA_2378|3end_Two-component_system_transcriptional_regulator,_LytR/AlgR_family,_putative_2383129..2383279_NEGATIVE 211 56 16 127 87 NC_009009:SSA_1316|3end_Nicotinamide_mononucleotide_transporter,_putative_1332157..1332307_NEGATIVE 203 59 15 102 63 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 202 49 7 70 29 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 200 73 31 104 64 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 198 50 15 145 110 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 191 49 1 132 88 NC_009009:SSA_2217|3end_Cps9H,_putative_2218086..2218236_NEGATIVE 189 44 7 147 101 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 189 47 9 82 42 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 188 80 36 86 33 NC_009009:SSA_0128|3end_Adenylate_kinase,_putative_119919..120069_POSITIVE 186 46 10 67 33 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 184 81 42 40 1 NC_009009:SSA_0858|3end_DTDP-L-rhamnose_synthase,_putative_846446..846596_POSITIVE 183 89 43 54 9 NC_009009:SSA_0774|3end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_756075..756225_POSITIVE 182 74 45 75 44 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE 181 57 11 138 100 NC_009009:SSA_2320|3end_hypothetical_protein_2322302..2322452_NEGATIVE 181 41 1 124 88 NC_009009:SSA_1107|3end_Lipid/multidrug/protein-type_ABC_exporter,_ATP_binding/membrane-spanning_protein,_putative_1133784..1133934_POSITIVE 180 78 35 68 19 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE