Origin IGS: atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat .........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 atcttcctccttttccttcctagtatagctcaattttctctttttgtatagacaattcttaattgcaagcattttatatatcacgagtcaggaactaatactgatagtgacaatgagatcgaatcgctcagtttgttccaaagccaaagaccaagaaatttttttcttaaagcatacaaaaagcccagtcaaactgagcttttgaattttttgat Mask Tandem Repeat Region ================================================ atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat Find is-nt database================================================ Query_seq: SSA_0192:SSA_0193|SSA_0192:SSA_0193:Acetate kinase, putative:CAAX amino terminal protease family protein, putative:->->:194243..194457 215 atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0192:SSA_0193|SSA_0192:SSA_0193:Acetate kinase, putative:CAAX amino terminal protease family protein, putative:->->:194243..194457 215 atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0192:SSA_0193|SSA_0192:SSA_0193:Acetate kinase, putative:CAAX amino terminal protease family protein, putative:->->:194243..194457 215 atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 9 End: 125 ........ M Q K L S L T G L F V C F K K K I S W S L A L E Q T E R F D L I V T I S I S S .......................................................................................... Protein_Len: 35 Strand: + Start: 28 End: 132 ........................... M G F L Y A L R K K F L G L W L W N K L S D S I S L S L S V L V P D S ................................................................................... Protein_Len: 53 Strand: - Start: 14 End: 172 ............. F S L K V P S K T H K L F F I E Q D K A K S C V S R N S R M T V I L I L E Q S T I Y L I S A I L F Q R Y M ........................................... Protein_Len: 53 Strand: - Start: 3 End: 161 .. L F N L L E T Q S P K K Y A K L F F N R P R Q S Q F L S L S E I E N D S D T N T G S E H Y I F H K C N L M ...................................................... atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat 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================================================ atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -6.5 Tail_Score: -4.5366 Start: 17 End: 33 Full_Region: taaagcatacaaaaa gcccagt caa actgagc ttttgaattttttga ................gcccagtcaaactgagc...................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0192:SSA_0193|SSA_0192:SSA_0193:Acetate kinase, putative:CAAX amino terminal protease family protein, putative:->->:194243..194457 215 atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat Intra-Species Hit: Count: 1 Min: 1 Max: 215 Len: 215 Subject: NC_009009_SSA_0192_SSA_0193|Acetate kinase, putative:CAAX amino terminal protease family protein, putative|POSITIVE:POSITIVE|[194243,194457]|215 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 215 Query Start:1 Query End:215 Subject Strand: POSITIVE Subject Start: 1 Subject End: 215 atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagnnnnnnntttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat atcaaaaaattcaaaagctcagtttgactgggctttttgtatgctttaagaaaaaaatttcttggtctttggctttggaacaaactgagcgattcgatctcattgtcactatcagtattagttcctgactcgtgatatataaaatgcttgcaattaagaattgtctatacaaaaagagaaaattgagctatactaggaaggaaaaggaggaagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAAAAAUUCAAAAGCUCAGUUUGACUGGGCUUUUUGUAUGCUUUAAGAAAAAAAUUUCUUGGUCUUUGGCUUUGGAACAAACUGAGCGAUUCGAUCUCAUUGUCACUAUCAGUAUUAGUUCCUGACUCGUGAUAUAUAAAAUGCUUGCAAUUAAGAAUUGUCUAUACAAAAAGAGAAAAUUGAGCUAUACUAGGAAGGAAAAGGAGGAAGAU ............((((((((((.....))))))))))......((((..........(((((((((...((((((.((((((((((((......((((...))))......))))).)).)))))...(((.((.((((...(((.((((....)))).)))...))))))....)))......)))))).))))))))).........)))).. (-45.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUCCUCCUUUUCCUUCCUAGUAUAGCUCAAUUUUCUCUUUUUGUAUAGACAAUUCUUAAUUGCAAGCAUUUUAUAUAUCACGAGUCAGGAACUAAUACUGAUAGUGACAAUGAGAUCGAAUCGCUCAGUUUGUUCCAAAGCCAAAGACCAAGAAAUUUUUUUCUUAAAGCAUACAAAAAGCCCAGUCAAACUGAGCUUUUGAAUUUUUUGAU .............................((((...((((..((((((.(((....)))....))))))...........((((..(((((.........))))).))))....))))(((((..((((((((((.................((((((....))))))...((.........)).....)))))))))).))))).....)))). (-37.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 140 100 228 189 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 315 130 84 209 172 NC_009009:SSA_0527|5end_Propanediol_utilization_protein_PduL_524625..524855_POSITIVE 288 100 56 145 106 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 287 42 1 149 110 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 282 110 62 155 108 NC_009009:SSA_0836|5end_SecA-like_protein,_putative_821508..821738_POSITIVE 278 124 81 216 170 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 276 98 57 125 70 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 271 109 61 69 10 NC_009009:SSA_0513|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_511558..511788_POSITIVE 270 134 107 28 1 NC_009009:SSA_1932|5end_Biotin_carboxylase,_putative_1920874..1921104_NEGATIVE 269 154 111 177 132 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 267 100 54 202 147 NC_009009:SSA_1900|5end_N_utilization_substance_protein_A,_putative_1896012..1896242_NEGATIVE 264 130 85 110 53 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 263 110 61 184 126 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 262 110 61 174 122 NC_009009:SSA_0795|5end_hypothetical_protein_776620..776850_POSITIVE 260 114 71 183 144 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 257 107 61 66 28 NC_009009:SSA_0631|5end_Tryptophan_synthase_beta_chain,_putative_619872..620102_POSITIVE 257 100 59 200 154 NC_009009:SSA_0321|5end_Methylase,_putative_313867..314097_POSITIVE 257 152 118 98 63 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 252 49 10 63 17 NC_009009:SSA_2200|5end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201573..2201803_NEGATIVE 251 103 61 67 25 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 100 56 143 104 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 287 42 1 107 68 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 269 154 111 135 90 NC_009009:SSA_2012|3end_hypothetical_protein_2012898..2013048_NEGATIVE 268 107 61 60 6 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 267 100 54 148 93 NC_009009:SSA_1901|3end_Conserved_uncharacterized_protein_1896066..1896216_NEGATIVE 261 98 58 137 82 NC_009009:SSA_1428|3end_hypothetical_protein_1435638..1435788_NEGATIVE 257 100 59 77 31 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE 257 152 118 101 66 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 256 78 32 102 43 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 255 109 61 56 3 NC_009009:SSA_0512|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_511625..511775_POSITIVE 251 103 61 74 32 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 245 66 26 48 7 NC_009009:SSA_0274|3end_hypothetical_protein_268580..268730_NEGATIVE 245 37 13 78 54 NC_009009:SSA_0192|3end_Acetate_kinase,_putative_194182..194332_POSITIVE 244 115 71 74 17 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 240 210 161 134 88 NC_009009:SSA_1624|3end_hypothetical_protein_1626497..1626647_POSITIVE 239 107 61 76 23 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 238 150 112 65 30 NC_009009:SSA_2372|3end_hypothetical_protein_2374285..2374435_POSITIVE 237 50 21 144 113 NC_009009:SSA_0183|3end_hypothetical_protein_188106..188256_POSITIVE 236 39 2 76 33 NC_009009:SSA_2257|3end_DNA_mismatch_repair_protein,_putative_2251241..2251391_NEGATIVE 233 79 36 148 106 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE