Origin IGS: ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaaaattcagaattatttaatttgttcgaatttggtttgtttaagttgacaaactgtataaaaacaattatagtagttgatgtagctagaatagagaggagtaagaa Mask Tandem Repeat Region ================================================ ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct Find is-nt database================================================ Query_seq: SSA_1964:SSA_1965|SSA_1964:SSA_1965:conserved uncharacterized protein:Stomatin/prohibitin-like membrane protease subunits, putative:<-<-:1961302..1961409 108 ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1964:SSA_1965|SSA_1964:SSA_1965:conserved uncharacterized protein:Stomatin/prohibitin-like membrane protease subunits, putative:<-<-:1961302..1961409 108 ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1964:SSA_1965|SSA_1964:SSA_1965:conserved uncharacterized protein:Stomatin/prohibitin-like membrane protease subunits, putative:<-<-:1961302..1961409 108 ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 16 End: 108 ............... M L A T S T T I I V F I Q F V N L N K P N S N K L N N S E F S ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct 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: 87 Start: 34 End: 63 .................................GTTGACAAACTGTATAAAAACAATTATAGT............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1964:SSA_1965|SSA_1964:SSA_1965:conserved uncharacterized protein:Stomatin/prohibitin-like membrane protease subunits, putative:<-<-:1961302..1961409 108 ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_009009_SSA_1964_SSA_1965|conserved uncharacterized protein:Stomatin/prohibitin-like membrane protease subunits, putative|NEGATIVE:NEGATIVE|[1961302,1961409]|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 ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct ttcttactcctctctattctagctacatcaactactataattgtttttatacagtttgtcaacttaaacaaaccaaattcgaacaaattaaataattctgaattttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUACUCCUCUCUAUUCUAGCUACAUCAACUACUAUAAUUGUUUUUAUACAGUUUGUCAACUUAAACAAACCAAAUUCGAACAAAUUAAAUAAUUCUGAAUUUUCU ........................................((((((..((...((((((........))))))...))..))))))...................... ( -7.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAUUCAGAAUUAUUUAAUUUGUUCGAAUUUGGUUUGUUUAAGUUGACAAACUGUAUAAAAACAAUUAUAGUAGUUGAUGUAGCUAGAAUAGAGAGGAGUAAGAA .............((((((..(((((((......((((((((......)))))))).........((((((...)))))).........)))))))...))))))... (-18.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 755 50 1 141 92 NC_009009:SSA_1964|5end_conserved_uncharacterized_protein_1961211..1961441_NEGATIVE 241 60 11 119 56 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 221 37 7 101 62 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 217 37 8 52 24 NC_009009:SSA_0183|5end_hypothetical_protein_187646..187876_POSITIVE 214 44 8 135 99 NC_009009:SSA_0342|5end_Pyruvate_formate-lyase,_putative_337206..337436_NEGATIVE 212 37 1 60 21 NC_009009:SSA_0914|5end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_924952..925182_POSITIVE 205 34 1 217 187 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 203 57 12 127 86 NC_009009:SSA_1056|5end_Firmicute_fructose-1,6-bisphosphatase,_putative_1071760..1071990_POSITIVE 202 50 1 78 22 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 197 62 23 122 86 NC_009009:SSA_1101|5end_Multidrug_resistance_efflux_pump/hemolysin_secretion_transmembrane_protein,_putative_1121911..1122141_POSITIVE 196 64 35 42 16 NC_009009:SSA_2078|5end_hypothetical_protein_2083837..2084067_NEGATIVE 195 50 2 121 74 NC_009009:SSA_0995|5end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_995716..995946_POSITIVE 195 56 19 84 45 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 195 43 5 175 132 NC_009009:SSA_0777|5end_Glycogen_biosynthesis_protein_GlgD,_putative_759430..759660_POSITIVE 192 38 6 57 16 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 191 50 8 142 98 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 191 50 3 91 46 NC_009009:SSA_0830|5end_Glycosyltransferase,_putative_812430..812660_POSITIVE 188 60 11 128 84 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 188 50 1 147 91 NC_009009:SSA_0246|5end_Conserved_uncharacterized_protein_239703..239933_POSITIVE 186 29 7 92 65 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 43 8 59 19 NC_009009:SSA_1482|3end_Pullulanase,_putative_1486949..1487099_NEGATIVE 203 57 12 84 43 NC_009009:SSA_1055|3end_Conserved_uncharacterized_protein_1071797..1071947_POSITIVE 196 36 2 38 9 NC_009009:SSA_0042|3end_Amino_acid_recemase,_putative_48671..48821_POSITIVE 186 29 7 33 6 NC_009009:SSA_0538|3end_PduH_protein,_putative_534254..534404_POSITIVE 183 100 58 129 90 NC_009009:SSA_0331|3end_C3-degrading_proteinase,_putative_325992..326142_POSITIVE 182 44 7 128 103 NC_009009:SSA_0040|3end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_47479..47629_POSITIVE 181 65 21 58 19 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 181 25 1 126 97 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 180 60 12 117 78 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 180 28 1 139 111 NC_009009:SSA_1252|3end_hypothetical_protein_1276771..1276921_NEGATIVE 179 36 1 95 59 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 179 80 31 139 86 NC_009009:SSA_1564|3end_Histidine_kinase,_putative_1567266..1567416_NEGATIVE 179 29 2 112 84 NC_009009:SSA_1003|3end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1005214..1005364_POSITIVE 177 30 7 124 96 NC_009009:SSA_0750|3end_hypothetical_protein_732255..732405_POSITIVE 176 48 1 127 78 NC_009009:SSA_1381|3end_hypothetical_protein_1399146..1399296_NEGATIVE 175 58 11 132 78 NC_009009:SSA_1809|3end_PTS_system_glucose-specific_EIIC_BA_component_(EIICBA-Glc)_(EII-_Glc/EIII-Glc),_putative_1792227..1792377_NEGATIVE 174 30 1 40 6 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 174 48 3 133 78 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 173 39 8 136 106 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 173 41 6 113 70 NC_009009:SSA_0455|3end_Sucrose-6-phosphate_hydrolase,_putative_456996..457146_NEGATIVE