Origin IGS: ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggaaacgcagcctcccttaggggaggttttttgattggaagaataatttatgttataatattgtaaaatttgtcattgtttttcaatgttttcgcaatatgacaaatcaataaaatttataaggagaaaacc Mask Tandem Repeat Region ================================================ ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta Find is-nt database================================================ Query_seq: SSA_2182:SSA_2183|SSA_2182:SSA_2183:hypothetical protein:Glucose-6-phosphate isomerase, putative:<-<-:2181111..2181244 134 ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2182:SSA_2183|SSA_2182:SSA_2183:hypothetical protein:Glucose-6-phosphate isomerase, putative:<-<-:2181111..2181244 134 ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2182:SSA_2183|SSA_2182:SSA_2183:hypothetical protein:Glucose-6-phosphate isomerase, putative:<-<-:2181111..2181244 134 ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta Predict ORF larger than 30AA ================================================ ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta 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: 88 Start: 74 End: 103 .........................................................................TTTGATTGGAAGAATAATTTATGTTATAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2182:SSA_2183|SSA_2182:SSA_2183:hypothetical protein:Glucose-6-phosphate isomerase, putative:<-<-:2181111..2181244 134 ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: NC_009009_SSA_2182_SSA_2183|hypothetical protein:Glucose-6-phosphate isomerase, putative|NEGATIVE:NEGATIVE|[2181111,2181244]|134 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta ggttttctccttataaattttattgatttgtcatattgcgaaaacattgaaaaacaatgacaaattttacaatattataacataaattattcttccaatcaaaaaacctcccctaagggaggctgcgtttccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUUUCUCCUUAUAAAUUUUAUUGAUUUGUCAUAUUGCGAAAACAUUGAAAAACAAUGACAAAUUUUACAAUAUUAUAACAUAAAUUAUUCUUCCAAUCAAAAAACCUCCCCUAAGGGAGGCUGCGUUUCCUA ((........((((((........((((((((((....(((.....))).......))))))))))........))))))..........................((((((....))))))........)).. (-20.99) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAAACGCAGCCUCCCUUAGGGGAGGUUUUUUGAUUGGAAGAAUAAUUUAUGUUAUAAUAUUGUAAAAUUUGUCAUUGUUUUUCAAUGUUUUCGCAAUAUGACAAAUCAAUAAAAUUUAUAAGGAGAAAACC ..(....)..((((((((....))))))))..((((((.(....(((((....))))).((((((..(((.....(((((.....))))).)))..))))))..).))))))...................... (-28.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 869 130 81 221 172 NC_009009:SSA_2182|5end_hypothetical_protein_2181020..2181250_NEGATIVE 269 126 95 64 29 NC_009009:SSA_1396|5end_hypothetical_protein_1410374..1410604_NEGATIVE 250 127 90 127 84 NC_009009:SSA_1843|5end_Histidine_kinase,_putative_1837491..1837721_NEGATIVE 247 128 90 67 26 NC_009009:SSA_2155|5end_hypothetical_protein_2156102..2156332_NEGATIVE 242 130 88 186 137 NC_009009:SSA_0770|5end_Ribonucleoside-diphosphate_reductase,_putative_751411..751641_NEGATIVE 236 129 102 88 53 NC_009009:SSA_0932|5end_hypothetical_protein_941453..941683_POSITIVE 234 130 102 116 92 NC_009009:SSA_2267|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2266127..2266357_POSITIVE 232 125 86 223 188 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 230 130 82 148 105 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 230 129 106 123 99 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 229 130 87 172 124 NC_009009:SSA_1352|5end_hypothetical_protein_1367941..1368171_NEGATIVE 228 130 94 130 87 NC_009009:SSA_1608|5end_hypothetical_protein_1613753..1613983_NEGATIVE 227 130 116 16 2 NC_009009:SSA_1222|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1245454..1245684_NEGATIVE 225 130 90 122 84 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 225 126 90 63 37 NC_009009:SSA_0459|5end_hypothetical_protein_462098..462328_POSITIVE 223 124 96 100 72 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 222 130 108 49 19 NC_009009:SSA_0286|5end_Transaldolase-like_protein,_putative_278814..279044_POSITIVE 219 128 87 61 12 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 219 126 81 118 70 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 217 128 92 208 170 NC_009009:SSA_0783|5end_Proton-translocating_ATPase,_F0_sector,_subunit_a,_putative_766815..767045_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 127 87 126 91 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 250 127 90 130 87 NC_009009:SSA_1844|3end_hypothetical_protein_1837488..1837638_NEGATIVE 232 125 86 125 90 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 230 130 82 144 101 NC_009009:SSA_1075|3end_Coproporphyrinogen_III_oxidase,_putative_1094303..1094453_POSITIVE 230 129 106 70 46 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 229 130 87 139 91 NC_009009:SSA_1353|3end_hypothetical_protein_1367974..1368124_NEGATIVE 225 130 90 141 103 NC_009009:SSA_1252|3end_hypothetical_protein_1276771..1276921_NEGATIVE 223 124 96 63 35 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 222 129 91 92 52 NC_009009:SSA_0771|3end_Glutaredoxin-like_protein,_putative_751572..751722_NEGATIVE 222 130 108 34 4 NC_009009:SSA_0285|3end_Formate_acetyltransferase_3,_putative_278879..279029_POSITIVE 220 122 84 81 38 NC_009009:SSA_0177|3end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_182132..182282_POSITIVE 219 128 87 68 19 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 219 129 99 62 34 NC_009009:SSA_1101|3end_Multidrug_resistance_efflux_pump/hemolysin_secretion_transmembrane_protein,_putative_1123199..1123349_POSITIVE 219 126 81 118 70 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 216 126 89 106 51 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 215 126 87 132 91 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 214 127 81 117 73 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 210 123 85 117 69 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 209 127 101 66 40 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 208 129 82 114 64 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE