Origin IGS: tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctattttctatcattatctaataaaaatcattaaaaagttaggaatttcctaacttttttgcttaatttgtgatataataaataaaaattttgaaaatagaaagttttctgaaa Mask Tandem Repeat Region ================================================ tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga Find is-nt database================================================ Query_seq: SSA_1181:SSA_1182|SSA_1181:SSA_1182:Hydrolase, alpha/beta superfamily, putative:Gid-like protein, putative:<-<-:1209507..1209621 115 tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1181:SSA_1182|SSA_1181:SSA_1182:Hydrolase, alpha/beta superfamily, putative:Gid-like protein, putative:<-<-:1209507..1209621 115 tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1181:SSA_1182|SSA_1181:SSA_1182:Hydrolase, alpha/beta superfamily, putative:Gid-like protein, putative:<-<-:1209507..1209621 115 tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga Predict ORF larger than 30AA ================================================ tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga 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: 81 Start: 11 End: 40 ..........CTTTCTATTTTCAAAATTTTTATTTATTAT........................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 84 HP_score: -10.5 Tail_Score: -2.62714 Start: 55 End: 83 Full_Region: TATCACAAATTAAGC AAAAAAGTTAGGA AAT TCCTAACTTTTTA ATGATTTTTATTAGA ......................................................AAAAAAGTTAGGAAATTCCTAACTTTTTA................................ TransTerm Strand: + Conf: 93 HP_score: -9.5 Tail_Score: -4.88129 Start: 61 End: 77 Full_Region: AAATTAAGCAAAAAA GTTAGGA AAT TCCTAAC TTTTTAATGATTTTT ............................................................GTTAGGAAATTCCTAAC...................................... Find igs database================================================ Query_seq: SSA_1181:SSA_1182|SSA_1181:SSA_1182:Hydrolase, alpha/beta superfamily, putative:Gid-like protein, putative:<-<-:1209507..1209621 115 tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_009009_SSA_1181_SSA_1182|Hydrolase, alpha/beta superfamily, putative:Gid-like protein, putative|NEGATIVE:NEGATIVE|[1209507,1209621]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga tttcagaaaactttctattttcaaaatttttatttattatatcacaaattaagcaaaaaagttaggaaattcctaactttttaatgatttttattagataatgatagaaaataga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAGAAAACUUUCUAUUUUCAAAAUUUUUAUUUAUUAUAUCACAAAUUAAGCAAAAAAGUUAGGAAAUUCCUAACUUUUUAAUGAUUUUUAUUAGAUAAUGAUAGAAAAUAGA .............(((((((((...(((.(((((((.((.((((...........(((((((((((.....)))))))))))..))))...)).))))))).))).))))))))) (-23.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUUUUCUAUCAUUAUCUAAUAAAAAUCAUUAAAAAGUUAGGAAUUUCCUAACUUUUUUGCUUAAUUUGUGAUAUAAUAAAUAAAAAUUUUGAAAAUAGAAAGUUUUCUGAAA (((((((((........................(((((((((((.....)))))))))))......((((((......)))))).........)))))))))............. (-22.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 661 90 41 181 132 NC_009009:SSA_1181|5end_Hydrolase,_alpha/beta_superfamily,_putative_1209416..1209646_NEGATIVE 243 69 28 140 93 NC_009009:SSA_1873|5end_S-adenosyl-methyltransferase_mraW,_putative_1870144..1870374_NEGATIVE 231 48 13 131 93 NC_009009:SSA_1715|5end_Phosphoserine_aminotransferase,_putative_1702488..1702718_NEGATIVE 214 60 28 114 82 NC_009009:SSA_2114|5end_Transcriptional_repressor_of_purine_operon,_putative_2117559..2117789_NEGATIVE 211 78 31 168 117 NC_009009:SSA_0718|5end_Conserved_uncharacterized_protein_703761..703991_POSITIVE 210 69 36 160 131 NC_009009:SSA_1917|5end_Alcohol_dehydrogenase,_propanol-preferring,_putative_1906517..1906747_POSITIVE 202 84 46 226 183 NC_009009:SSA_1979|5end_Alkaline-shock_protein,_putative_1974301..1974531_NEGATIVE 201 78 35 164 121 NC_009009:SSA_1864|5end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1860870..1861100_NEGATIVE 201 45 2 136 87 NC_009009:SSA_1421|5end_Adenine_phosphoribosyltransferase,_putative_1431285..1431515_NEGATIVE 200 78 40 231 189 NC_009009:SSA_0988|5end_TfoX_N-terminal_domain_family_protein,_putative_990662..990892_POSITIVE 193 53 11 145 98 NC_009009:SSA_2087|5end_Conserved_uncharacterized_protein_2092657..2092887_NEGATIVE 190 92 52 62 19 NC_009009:SSA_0927|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936049..936279_POSITIVE 189 74 34 137 96 NC_009009:SSA_1624|5end_hypothetical_protein_1626070..1626300_POSITIVE 188 54 15 141 95 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 186 91 55 148 114 NC_009009:SSA_0330|5end_hypothetical_protein_323799..324029_POSITIVE 185 58 33 112 87 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 184 44 1 223 179 NC_009009:SSA_2140|5end_Ribonuclease_P_protein_component,_putative_2140574..2140804_NEGATIVE 177 91 51 204 160 NC_009009:SSA_2015|5end_Phosphoglycerate_mutase,_putative_2015492..2015722_NEGATIVE 175 22 1 63 43 NC_009009:SSA_0774|5end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_754571..754801_POSITIVE 173 68 36 164 134 NC_009009:SSA_0135|5end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_130574..130804_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 97 51 57 14 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 245 97 52 72 25 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 225 82 41 87 42 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 214 60 28 51 19 NC_009009:SSA_2116|3end_Cmp-binding-factor_1,_putative_2117622..2117772_NEGATIVE 202 84 46 83 40 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 201 78 35 56 13 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 196 78 31 71 20 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 190 79 34 84 31 NC_009009:SSA_2014|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014019..2014169_NEGATIVE 187 77 61 129 113 NC_009009:SSA_0377|3end_ABC-type_methionine_transporter,_permease_component,_putative_367218..367368_POSITIVE 186 91 55 84 50 NC_009009:SSA_0329|3end_Glycerol_uptake_facilitator/aquaporin_protein,_putative_323815..323965_POSITIVE 178 99 51 91 46 NC_009009:SSA_0773|3end_PTS_enzyme_I,_putative_754416..754566_POSITIVE 177 91 51 104 60 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 177 45 11 39 1 NC_009009:SSA_1422|3end_hypothetical_protein_1431382..1431532_NEGATIVE 177 65 24 50 8 NC_009009:SSA_0572|3end_Dehydrogenase,_putative_568552..568702_POSITIVE 174 82 42 86 36 NC_009009:SSA_1373|3end_ATPase_components_of_ABC_transporters_with_duplicated_ATPase_domains,_multidrug_transport_system,_putative_1391313..1391463_POSITIVE 171 46 5 100 60 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 169 86 48 72 27 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 168 82 46 90 52 NC_009009:SSA_0680|3end_Serine/threonine_protein_phosphatase,_putative_663233..663383_POSITIVE 165 82 52 90 61 NC_009009:SSA_0015|3end_Membrane_ATPase_FtsH,_degrades_sigma32_(integral_membrane_cell-division_Zn_metallo-peptidase),_putative_15097..15247_POSITIVE 157 94 60 119 89 NC_009009:SSA_2038|3end_hypothetical_protein_2042669..2042819_POSITIVE