Origin IGS: ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga .........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 tcaaaagcatgctctgctattattttcgtataacagtttcaaaatagtaaaaactactctagcacaaaaagtttgtgaaatttctattttggtatcgaaaaccagtttatccaatggattgactggtttttctttgtgaaatataagtgagcaaaagttttgacagtgcttacagctttagatagaattaagtagaagaattatgcttagaaaggcaaaaaa Mask Tandem Repeat Region ================================================ ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga Find is-nt database================================================ Query_seq: SSA_1178:SSA_1179|SSA_1178:SSA_1179:Acetoin dehydrogenase, E1 component, alpha subunit, putative:Carbamoylphosphate synthase large subunit / biotin carboxylase, putative:<-<-:1206508..1206729 222 ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1178:SSA_1179|SSA_1178:SSA_1179:Acetoin dehydrogenase, E1 component, alpha subunit, putative:Carbamoylphosphate synthase large subunit / biotin carboxylase, putative:<-<-:1206508..1206729 222 ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1178:SSA_1179|SSA_1178:SSA_1179:Acetoin dehydrogenase, E1 component, alpha subunit, putative:Carbamoylphosphate synthase large subunit / biotin carboxylase, putative:<-<-:1206508..1206729 222 ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 35 End: 136 .................................. M L S K A V S T V K T F A H L Y F T K K N Q S I H W I N W F S I P K ...................................................................................... Protein_Len: 48 Strand: + Start: 79 End: 219 .............................................................................. M F H K E K P V N P L D K L V F D T K I E I S Q T F C A R V V F T I L K L L Y E N N S R A C F * ... Protein_Len: 41 Strand: - Start: 87 End: 209 ...................................................................................... L S F G T L G N S L S T K S V L I S I E C V K Q A L T T K V I K F S N Y S F L L M ............. ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga 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: 89 Start: 35 End: 64 ..................................TTTGACAGTGCTTACAGCTTTAGATAGAAT.............................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -7.1 Tail_Score: -4.18018 Start: 97 End: 121 Full_Region: TTTCACAAAGAAAAA CCAGTCAATCC ATT GGATAAACTGG TTTTCGATACCAAAA ................................................................................................CCAGTCAATCCATTGGATAAACTGG..................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -9.3 Tail_Score: -5.38054 Start: 97 End: 121 Full_Region: ttttggtatcgaaaa ccagtttatcc aat ggattgactgg tttttctttgtgaaa ................................................................................................ccagtttatccaatggattgactgg..................................................................................................... Find igs database================================================ Query_seq: SSA_1178:SSA_1179|SSA_1178:SSA_1179:Acetoin dehydrogenase, E1 component, alpha subunit, putative:Carbamoylphosphate synthase large subunit / biotin carboxylase, putative:<-<-:1206508..1206729 222 ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga Intra-Species Hit: Count: 1 Min: 1 Max: 222 Len: 222 Subject: NC_009009_SSA_1178_SSA_1179|Acetoin dehydrogenase, E1 component, alpha subunit, putative:Carbamoylphosphate synthase large subunit / biotin carboxylase, putative|NEGATIVE:NEGATIVE|[1206508,1206729]|222 HSP 1 e-value: 1.0E-123 bit: 440.0 Len: 222 Query Start:1 Query End:222 Subject Strand: POSITIVE Subject Start: 1 Subject End: 222 ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga ttttttgcctttctaagcataattcttctacttaattctatctaaagctgtaagcactgtcaaaacttttgctcacttatatttcacaaagaaaaaccagtcaatccattggataaactggttttcgataccaaaatagaaatttcacaaactttttgtgctagagtagtttttactattttgaaactgttatacgaaaataatagcagagcatgcttttga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUGCCUUUCUAAGCAUAAUUCUUCUACUUAAUUCUAUCUAAAGCUGUAAGCACUGUCAAAACUUUUGCUCACUUAUAUUUCACAAAGAAAAACCAGUCAAUCCAUUGGAUAAACUGGUUUUCGAUACCAAAAUAGAAAUUUCACAAACUUUUUGUGCUAGAGUAGUUUUUACUAUUUUGAAACUGUUAUACGAAAAUAAUAGCAGAGCAUGCUUUUGA ...........((.((((((.......((((((..((((((........((.((((..((....))...)))).))..............(((((.(((((..((((...))))..)))))))))).........))))))....(((((.....)))))...)))))).................(((((((.........)))))))...))))))..)) (-40.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAAGCAUGCUCUGCUAUUAUUUUCGUAUAACAGUUUCAAAAUAGUAAAAACUACUCUAGCACAAAAAGUUUGUGAAAUUUCUAUUUUGGUAUCGAAAACCAGUUUAUCCAAUGGAUUGACUGGUUUUUCUUUGUGAAAUAUAAGUGAGCAAAAGUUUUGACAGUGCUUACAGCUUUAGAUAGAAUUAAGUAGAAGAAUUAUGCUUAGAAAGGCAAAAAA ....(((((((.(((..(((((((((...((....))...)))))))))....(((((....(((((.....)))))....((((((((.(((...(((((((((((.((((...)))).)))))))))))...............(((((((...((....))..))))))).)))..))))))))...))))).)))..))))))).............. (-51.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 120 71 211 162 NC_009009:SSA_1178|5end_Acetoin_dehydrogenase,_E1_component,_alpha_subunit,_putative_1206417..1206647_NEGATIVE 277 109 71 230 203 NC_009009:SSA_1620|5end_Uridylate_kinase,_putative_1622981..1623211_NEGATIVE 274 133 96 128 98 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 266 85 43 98 59 NC_009009:SSA_0900|5end_Tetratricopeptide_repeat_(TPR)_family_protein_891068..891298_POSITIVE 252 100 52 172 126 NC_009009:SSA_2032|5end_Integrase/recombinase,_phage_integrase_family,_putative_2038006..2038236_POSITIVE 252 85 44 215 172 NC_009009:SSA_1586|5end_hypothetical_protein_1588182..1588412_NEGATIVE 248 62 23 138 102 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 246 78 31 69 26 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 244 48 3 223 177 NC_009009:SSA_0557|5end_hypothetical_protein_551900..552130_POSITIVE 243 133 98 56 16 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 243 122 90 128 92 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 240 80 31 160 117 NC_009009:SSA_1453|5end_hypothetical_protein_1460208..1460438_NEGATIVE 239 137 96 230 188 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 237 63 27 162 129 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 232 59 11 182 143 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 230 198 152 76 25 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 228 75 44 210 174 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 227 86 47 66 22 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 227 44 7 94 50 NC_009009:SSA_1060|5end_hypothetical_protein_1076765..1076995_POSITIVE 226 85 41 205 157 NC_009009:SSA_2015|5end_Phosphoglycerate_mutase,_putative_2015492..2015722_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 120 71 54 12 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 274 133 96 46 16 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 266 85 43 111 72 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 259 78 38 38 2 NC_009009:SSA_0971|3end_Conserved_uncharacterized_protein_980069..980219_POSITIVE 248 62 23 151 115 NC_009009:SSA_1012|3end_Phosphoenolpyruvate_synthase,_putative_1017314..1017464_POSITIVE 246 78 31 59 16 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 243 133 98 54 14 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE 241 85 41 81 32 NC_009009:SSA_0766|3end_hypothetical_protein_746975..747125_POSITIVE 240 80 31 113 70 NC_009009:SSA_1454|3end_hypothetical_protein_1460255..1460405_NEGATIVE 237 63 27 128 95 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 228 70 21 99 36 NC_009009:SSA_0172|3end_Transcriptional_regulator,_XRE_family,_putative_169672..169822_POSITIVE 226 85 41 105 57 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 226 78 33 61 23 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 221 62 22 142 100 NC_009009:SSA_1821|3end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810047..1810197_NEGATIVE 218 190 143 80 28 NC_009009:SSA_2316|3end_General_secretory_pathway_protein_F,_putative_2317116..2317266_NEGATIVE 217 140 93 131 79 NC_009009:SSA_2166|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2163873..2164023_NEGATIVE 217 77 34 131 83 NC_009009:SSA_1297|3end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1313141..1313291_NEGATIVE 217 71 33 116 81 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 217 158 111 69 18 NC_009009:SSA_0541|3end_Acetate_kinase,_putative_537082..537232_POSITIVE 216 134 92 69 20 NC_009009:SSA_1066|3end_ABC-type_oligopeptide_transport_system,_putative_1086376..1086526_POSITIVE