Origin IGS: ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atctgtatctgatctttccaaaaacaagccacataacggatttatgtagcttgttattttctctttgaaagaaatatgctaaattactttatttcttaattacattat Mask Tandem Repeat Region ================================================ ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat Find is-nt database================================================ Query_seq: SSA_1168:SSA_1169|SSA_1168:SSA_1169:hypothetical protein:Conserved hypothetical protein with an alpha/beta hydrolase fold, putative:->->:1195983..1196090 108 ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1168:SSA_1169|SSA_1168:SSA_1169:hypothetical protein:Conserved hypothetical protein with an alpha/beta hydrolase fold, putative:->->:1195983..1196090 108 ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1168:SSA_1169|SSA_1168:SSA_1169:hypothetical protein:Conserved hypothetical protein with an alpha/beta hydrolase fold, putative:->->:1195983..1196090 108 ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat Predict ORF larger than 30AA ================================================ ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat 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================================================ ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.2 Tail_Score: -4.57569 Start: 56 End: 84 Full_Region: TCAAAGAGAAAATAA CAAGCTACATAA ATCCG TTATGTGGCTTG TTTTTGGAAAGATCA .......................................................CAAGCTACATAAATCCGTTATGTGGCTTG........................ Find igs database================================================ Query_seq: SSA_1168:SSA_1169|SSA_1168:SSA_1169:hypothetical protein:Conserved hypothetical protein with an alpha/beta hydrolase fold, putative:->->:1195983..1196090 108 ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_009009_SSA_1168_SSA_1169|hypothetical protein:Conserved hypothetical protein with an alpha/beta hydrolase fold, putative|POSITIVE:POSITIVE|[1195983,1196090]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat ataatgtaattaagaaataaagtaatttagcatatttctttcaaagagaaaataacaagctacataaatccgttatgtggcttgtttttggaaagatcagatacagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUGUAAUUAAGAAAUAAAGUAAUUUAGCAUAUUUCUUUCAAAGAGAAAAUAACAAGCUACAUAAAUCCGUUAUGUGGCUUGUUUUUGGAAAGAUCAGAUACAGAU ....((((.....(...((((....)))).).....((((((...((((.....(((((((((((((.....))))))))))))))))).)))))).....))))... (-25.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUGUAUCUGAUCUUUCCAAAAACAAGCCACAUAACGGAUUUAUGUAGCUUGUUAUUUUCUCUUUGAAAGAAAUAUGCUAAAUUACUUUAUUUCUUAAUUACAUUAU ...((((...............(((((((.((((((.....)))))).))))))).............((((((((.............))))))))...)))).... (-19.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 223 99 62 167 129 NC_009009:SSA_0658|5end_Conserved_uncharacterized_protein_642126..642356_POSITIVE 220 100 63 34 1 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 207 98 68 32 2 NC_009009:SSA_0263|5end_Zinc_metalloproteinase_in_scaA_5'region,_putative_256274..256504_POSITIVE 206 89 44 114 72 NC_009009:SSA_1059|5end_hypothetical_protein_1076153..1076383_POSITIVE 205 84 47 162 128 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 198 92 68 33 8 NC_009009:SSA_0358|5end_hypothetical_protein_351797..352027_NEGATIVE 198 91 56 67 33 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 198 97 75 218 191 NC_009009:SSA_0048|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_53443..53673_NEGATIVE 197 88 69 230 211 NC_009009:SSA_1751|5end_Dextran_glucosidase,_alpha_amylase_family,_putative_1739801..1740031_NEGATIVE 197 96 56 190 148 NC_009009:SSA_0980|5end_3-isopropylmalate_dehydratase_large_subunit,_putative_984004..984234_POSITIVE 196 100 58 67 11 NC_009009:SSA_1672|5end_hypothetical_protein_1670389..1670619_NEGATIVE 195 91 58 74 29 NC_009009:SSA_2330|5end_Acetyltransferase,_putative_2333655..2333885_NEGATIVE 195 91 59 190 152 NC_009009:SSA_1583|5end_6-O-methylguanine-DNA_methyltransferase,_putative_1586026..1586256_NEGATIVE 195 97 68 171 143 NC_009009:SSA_0093|5end_V-type_sodium_ATPase,_subunit_D,_putative_94286..94516_POSITIVE 194 91 63 188 162 NC_009009:SSA_1121|5end_Cytochrome_C-type_biogenesis_protein,_putative_1147149..1147379_POSITIVE 194 96 56 186 140 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 192 98 59 66 27 NC_009009:SSA_0615|5end_RggD,_putative_609195..609425_NEGATIVE 189 100 75 207 177 NC_009009:SSA_2376|5end_ABC_transporter_with_duplicated_ATPase_domains,_putative_2378744..2378974_POSITIVE 189 92 61 220 182 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 189 97 57 51 7 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 96 54 54 5 NC_009009:SSA_1168|3end_hypothetical_protein_1195922..1196072_POSITIVE 295 88 41 88 31 NC_009009:SSA_0276|3end_Glycosyltransferase,_family_2/glycosyltransferase_family_8,_putative_270667..270817_POSITIVE 293 89 46 70 13 NC_009009:SSA_0277|3end_Pyruvate_formate-lyase_3,_putative_270708..270858_NEGATIVE 285 100 54 97 37 NC_009009:SSA_0288|3end_hypothetical_protein_280740..280890_NEGATIVE 268 90 46 145 83 NC_009009:SSA_2152|3end_ABC-type_transporter_(uncharacterized),_ATPase_component,_putative_2153043..2153193_NEGATIVE 248 88 54 79 35 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 220 100 63 41 8 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 211 99 55 128 81 NC_009009:SSA_1594|3end_Metalloendopeptidase,_putative_1598457..1598607_NEGATIVE 211 92 62 151 119 NC_009009:SSA_0657|3end_PyridoxaL_5'-phosphate_Dependent_Enzymes_class_III,_putative_642196..642346_POSITIVE 206 89 44 92 50 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 205 84 41 102 50 NC_009009:SSA_1617|3end_hypothetical_protein_1620436..1620586_NEGATIVE 189 92 61 77 39 NC_009009:SSA_1702|3end_hypothetical_protein_1692197..1692347_NEGATIVE 189 89 49 128 73 NC_009009:SSA_1192|3end_hypothetical_protein_1218435..1218585_NEGATIVE 187 91 58 81 53 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 186 96 51 55 3 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 185 98 58 108 64 NC_009009:SSA_1775|3end_Potassium_uptake_protein,_Trk_family,_putative_1762713..1762863_POSITIVE 184 92 57 31 4 NC_009009:SSA_0481|3end_Cobyric_acid_synthase,_putative_483541..483691_POSITIVE 181 98 69 150 113 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 180 96 59 139 104 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 178 85 42 66 30 NC_009009:SSA_0701|3end_Cation_transporter_CorA_family,_putative_685356..685506_POSITIVE