Origin IGS: tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaaacggattaatttcgaaagtttggacaaatgtacttgtcaaacgtcaagttttttggtaatataggaaagtatgtggtgctagcacatccgtaatattagatctaataggaggaaatacgata Mask Tandem Repeat Region ================================================ tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc Find is-nt database================================================ Query_seq: SSA_1980:SSA_1981|SSA_1980:SSA_1981:50S ribosomal protein L28, putative:hypothetical protein:<-<-:1974723..1974848 126 tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1980:SSA_1981|SSA_1980:SSA_1981:50S ribosomal protein L28, putative:hypothetical protein:<-<-:1974723..1974848 126 tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1980:SSA_1981|SSA_1980:SSA_1981:50S ribosomal protein L28, putative:hypothetical protein:<-<-:1974723..1974848 126 tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc Predict ORF larger than 30AA ================================================ tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc 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: 84 Start: 61 End: 90 ............................................................CTTGTCAAACGTCAAGTTTTTTGGTAATAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1980:SSA_1981|SSA_1980:SSA_1981:50S ribosomal protein L28, putative:hypothetical protein:<-<-:1974723..1974848 126 tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_009009_SSA_1980_SSA_1981|50S ribosomal protein L28, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1974723,1974848]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc tatcgtatttcctcctattagatctaatattacggatgtgctagcaccacatactttcctatattaccaaaaaacttgacgtttgacaagtacatttgtccaaactttcgaaattaatccgttttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCGUAUUUCCUCCUAUUAGAUCUAAUAUUACGGAUGUGCUAGCACCACAUACUUUCCUAUAUUACCAAAAAACUUGACGUUUGACAAGUACAUUUGUCCAAACUUUCGAAAUUAAUCCGUUUUC ...............(((((....)))))..(((((((((....)))............................((((.((((((((((....))))).)))))..)))).....)))))).... (-16.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAACGGAUUAAUUUCGAAAGUUUGGACAAAUGUACUUGUCAAACGUCAAGUUUUUUGGUAAUAUAGGAAAGUAUGUGGUGCUAGCACAUCCGUAAUAUUAGAUCUAAUAGGAGGAAAUACGAUA ....((.((..(((((.((..(((((.((((......))))))))).)))))))..)).))...........((((...(((....))).(((....(((((....)))))...))).)))).... (-21.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 892 60 11 151 102 NC_009009:SSA_1980|5end_50S_ribosomal_protein_L28,_putative_1974632..1974862_NEGATIVE 281 53 15 181 138 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 254 38 3 126 88 NC_009009:SSA_1548|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1551610..1551840_NEGATIVE 252 49 11 136 102 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 243 46 7 63 24 NC_009009:SSA_0427|5end_DNA-binding_transcriptional_activator,_SARP_family,_putative_424497..424727_POSITIVE 240 49 5 132 88 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 237 45 3 130 88 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 230 68 33 99 58 NC_009009:SSA_0961|5end_Possible_ketopantoate_reductase_PanE/ApbA,_putative_969913..970143_POSITIVE 225 59 14 58 12 NC_009009:SSA_2097|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102918..2103148_NEGATIVE 223 48 3 211 167 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 223 59 32 100 71 NC_009009:SSA_0168|5end_hypothetical_protein_166457..166687_POSITIVE 222 70 22 112 59 NC_009009:SSA_1236|5end_Mutator_protein,_putative_1261704..1261934_NEGATIVE 221 99 73 34 8 NC_009009:SSA_1969|5end_Acetolactate_synthase_small_subunit,_putative_1965222..1965452_NEGATIVE 221 60 11 147 97 NC_009009:SSA_0213|5end_hypothetical_protein_210135..210365_NEGATIVE 218 100 54 89 29 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 217 50 2 225 173 NC_009009:SSA_1515|5end_hypothetical_protein_1522129..1522359_NEGATIVE 215 48 3 134 88 NC_009009:SSA_2177|5end_hypothetical_protein_2176215..2176445_NEGATIVE 215 58 12 173 124 NC_009009:SSA_0482|5end_ATP:cobalamin_adenosyl_transferase,_putative_483458..483688_POSITIVE 214 69 23 105 60 NC_009009:SSA_2200|5end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201573..2201803_NEGATIVE 214 48 4 179 128 NC_009009:SSA_0777|5end_Glycogen_biosynthesis_protein_GlgD,_putative_759430..759660_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 99 51 41 1 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 240 49 5 145 101 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 237 45 3 133 91 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 230 68 33 83 42 NC_009009:SSA_0960|3end_Sensor_protein_ciaH,_putative_969977..970127_POSITIVE 223 48 5 112 69 NC_009009:SSA_1902|3end_tRNA_(guanine-N(7)-)-methyltransferase,_putative_1896753..1896903_NEGATIVE 222 70 22 103 50 NC_009009:SSA_1237|3end_Uracil-DNA_glycosylase,_putative_1261713..1261863_NEGATIVE 218 100 54 76 16 NC_009009:SSA_0432|3end_Formate--tetrahydrofolate_ligase,_putative_433288..433438_NEGATIVE 215 48 3 61 15 NC_009009:SSA_2178|3end_hypothetical_protein_2176288..2176438_NEGATIVE 211 35 3 116 78 NC_009009:SSA_0659|3end_hypothetical_protein_643868..644018_POSITIVE 207 60 24 31 1 NC_009009:SSA_1857|3end_Conserved_DivIVA-like_protein,_putative_1852725..1852875_NEGATIVE 206 48 3 125 67 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 205 60 20 75 31 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 204 77 33 52 4 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 204 47 5 126 95 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 203 59 14 45 9 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 201 70 38 53 17 NC_009009:SSA_1261|3end_Ribose-5-phosphate_isomerase_A,_putative_1286977..1287127_NEGATIVE 198 113 82 51 18 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 198 70 24 115 73 NC_009009:SSA_1553|3end_Permease,_putative_1556032..1556182_POSITIVE 198 45 3 130 75 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 197 79 34 78 38 NC_009009:SSA_2230|3end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2228963..2229113_NEGATIVE