Origin IGS: tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcgccatctttgttcttagtgctaatgtaaaaacataaataaagtgactagctagtattattttacggataaaaaacatagtagaaatgcctataaaataaggattcctgcaaattgctaagaatcctatttcctttcgcgtgtcagga Mask Tandem Repeat Region ================================================ tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga Find is-nt database================================================ Query_seq: SSA_0294:SSA_0295|SSA_0294:SSA_0295:hypothetical protein:Transcriptional regulator, LysR family, putative:<-<-:287967..288115 149 tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0294:SSA_0295|SSA_0294:SSA_0295:hypothetical protein:Transcriptional regulator, LysR family, putative:<-<-:287967..288115 149 tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0294:SSA_0295|SSA_0294:SSA_0295:hypothetical protein:Transcriptional regulator, LysR family, putative:<-<-:287967..288115 149 tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 20 End: 148 ................... M G F L A I C R N P Y F I G I S T M F F I R K I I L A S H F I Y V F T L A L R T K M A . tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga 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================================================ tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0294:SSA_0295|SSA_0294:SSA_0295:hypothetical protein:Transcriptional regulator, LysR family, putative:<-<-:287967..288115 149 tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: NC_009009_SSA_0294_SSA_0295|hypothetical protein:Transcriptional regulator, LysR family, putative|NEGATIVE:NEGATIVE|[287967,288115]|149 HSP 1 e-value: 2.0E-79 bit: 295.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga tcctgacacgcgaaaggaaataggattcttagcaatttgcaggaatccttattttataggcatttctactatgttttttatccgtaaaataatactagctagtcactttatttatgtttttacattagcactaagaacaaagatggcga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUGACACGCGAAAGGAAAUAGGAUUCUUAGCAAUUUGCAGGAAUCCUUAUUUUAUAGGCAUUUCUACUAUGUUUUUUAUCCGUAAAAUAAUACUAGCUAGUCACUUUAUUUAUGUUUUUACAUUAGCACUAAGAACAAAGAUGGCGA ...((((..((.....((((((((((((((.((.....)))))))))).))))))....))....(((.(((...(((((....)))))..))).)))...))))..((((((.((((((((.........)))))))).))))))... (-29.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGCCAUCUUUGUUCUUAGUGCUAAUGUAAAAACAUAAAUAAAGUGACUAGCUAGUAUUAUUUUACGGAUAAAAAACAUAGUAGAAAUGCCUAUAAAAUAAGGAUUCCUGCAAAUUGCUAAGAAUCCUAUUUCCUUUCGCGUGUCAGGA ...((..(((((((.....(((....)))........))))))).(((..((..(((......)))(((........((((((....)).))))......(((((((..((.....))...)))))))...)))....))..))).)). (-25.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 904 50 1 141 92 NC_009009:SSA_0294|5end_hypothetical_protein_287876..288106_NEGATIVE 247 66 22 185 137 NC_009009:SSA_0836|5end_SecA-like_protein,_putative_821508..821738_POSITIVE 245 47 4 197 149 NC_009009:SSA_1005|5end_Sugar_ABC_transporter,_permease_protein,_putative_1006028..1006258_POSITIVE 242 36 1 227 183 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 241 67 21 99 47 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 233 67 21 156 117 NC_009009:SSA_0577|5end_Ancient_RNA-binding_IF3-C_fold_(CRS1/YhbY_domain),_putative_571253..571483_POSITIVE 231 69 26 58 8 NC_009009:SSA_2224|5end_Phosphotyrosine-protein_phosphatase,_putative_2225442..2225672_NEGATIVE 231 50 1 155 110 NC_009009:SSA_1445|5end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447886..1448116_NEGATIVE 229 50 9 212 168 NC_009009:SSA_2291|5end_hypothetical_protein_2293204..2293434_POSITIVE 227 107 68 215 171 NC_009009:SSA_0819|5end_hypothetical_protein_800418..800648_POSITIVE 226 47 2 196 148 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 226 49 1 180 115 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 225 50 1 59 3 NC_009009:SSA_1877|5end_hypothetical_protein_1871659..1871889_POSITIVE 225 69 26 97 49 NC_009009:SSA_0529|5end_Ethanolamine_utilization_protein,_putative_525945..526175_POSITIVE 225 70 22 104 55 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 224 46 2 80 34 NC_009009:SSA_1359|5end_Arginine/histidine_ABC_transporter,_permease_component,_putative_1374182..1374412_POSITIVE 223 49 10 82 48 NC_009009:SSA_1525|5end_Lyzozyme_M1_(1,4-beta-N-acetylmuramidase),_putative_1532746..1532976_POSITIVE 221 132 94 172 137 NC_009009:SSA_1487|5end_Conserved_uncharacterized_protein_1494190..1494420_NEGATIVE 219 48 3 175 128 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 219 41 1 69 30 NC_009009:SSA_0427|5end_DNA-binding_transcriptional_activator,_SARP_family,_putative_424497..424727_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 48 2 83 30 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 241 67 21 84 32 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 233 67 21 48 9 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 231 69 26 61 11 NC_009009:SSA_2225|3end_Transcriptional_attenuator_LytR,_putative_2225439..2225589_NEGATIVE 231 50 1 143 98 NC_009009:SSA_1446|3end_Histidinol_dehydrogenase,_putative_1447898..1448048_NEGATIVE 230 46 1 138 101 NC_009009:SSA_0390|3end_hypothetical_protein_385714..385864_POSITIVE 227 62 36 146 117 NC_009009:SSA_0723|3end_hypothetical_protein_708466..708616_POSITIVE 227 50 1 85 24 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 225 50 1 62 6 NC_009009:SSA_1876|3end_hypothetical_protein_1871742..1871892_POSITIVE 225 69 26 82 34 NC_009009:SSA_0528|3end_Conserved_uncharacterized_protein_526010..526160_POSITIVE 225 70 22 95 46 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 224 50 1 103 55 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 217 47 1 63 5 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 213 61 25 70 29 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 210 48 1 144 103 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 208 48 2 138 78 NC_009009:SSA_1186|3end_Acetyltransferase,_CysE/LacA/Lpx_A/NodL_family,_putative_1214656..1214806_NEGATIVE 208 64 26 61 20 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 207 47 21 27 2 NC_009009:SSA_1233|3end_Membrane_protein,_YqiH_family,_putative_1257626..1257776_POSITIVE 205 85 46 80 37 NC_009009:SSA_2019|3end_hypothetical_protein_2018812..2018962_NEGATIVE 205 49 2 63 17 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE