Origin IGS: ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa .........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 ttttgctgaatcttattttataatcttctttcaaaacaatcaagtctttaaaacttttgttataaagatgtaaactatcacaatcttgtgataagaaataagagtgaagttaggaaaaatagttataagcagaaaaacaaatatttttatgtgctgaaaaatcttgatactgggtcttttattgctgaaatatttacttctttttatgataaaactgacttttgggccagaa Mask Tandem Repeat Region ================================================ ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa Find is-nt database================================================ Query_seq: SSA_0393:SSA_0394|SSA_0393:SSA_0394:Bacteriocin ABC-type exporter, ATP binding/permease protein, putative:hypothetical protein:->->:390481..390712 232 ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0393:SSA_0394|SSA_0393:SSA_0394:Bacteriocin ABC-type exporter, ATP binding/permease protein, putative:hypothetical protein:->->:390481..390712 232 ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0393:SSA_0394|SSA_0393:SSA_0394:Bacteriocin ABC-type exporter, ATP binding/permease protein, putative:hypothetical protein:->->:390481..390712 232 ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 23 End: 190 ...................... M I K R S K Y F S N K R P S I K I F Q H I K I F V F L L I T I F P N F T L I S Y H K I V I V Y I F I T K V L K T .......................................... Protein_Len: 48 Strand: - Start: 2 End: 145 . R A W F D T K D Y F S T F I E A I F S G T D L N K L V Y F Y K N K Q K Y S N K R V E S K N R I M ....................................................................................... ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa 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: 85 Start: 23 End: 52 ......................ATTGCTGAAATATTTACTTCTTTTTATGAT.................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 189 End: 218 ............................................................................................................................................................................................CTTGATTGTTTTGAAAGAAGATTATAAAAT.............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0393:SSA_0394|SSA_0393:SSA_0394:Bacteriocin ABC-type exporter, ATP binding/permease protein, putative:hypothetical protein:->->:390481..390712 232 ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: NC_009009_SSA_0393_SSA_0394|Bacteriocin ABC-type exporter, ATP binding/permease protein, putative:hypothetical protein|POSITIVE:POSITIVE|[390481,390712]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa ttctggcccaaaagtcagttttatcataaaaagaagtaaatatttcagcaataaaagacccagtatcaagatttttcagcacataaaaatatttgtttttctgcttataactatttttcctaacttcactcttatttcttatcacaagattgtgatagtttacatctttataacaaaagttttaaagacttgattgttttgaaagaagattataaaataagattcagcaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGGCCCAAAAGUCAGUUUUAUCAUAAAAAGAAGUAAAUAUUUCAGCAAUAAAAGACCCAGUAUCAAGAUUUUUCAGCACAUAAAAAUAUUUGUUUUUCUGCUUAUAACUAUUUUUCCUAACUUCACUCUUAUUUCUUAUCACAAGAUUGUGAUAGUUUACAUCUUUAUAACAAAAGUUUUAAAGACUUGAUUGUUUUGAAAGAAGAUUAUAAAAUAAGAUUCAGCAAAA ...((((..(((((((................(((((....)))))..........((.......))..)))))))..)).))........((((((..(((..((((((((.((((((..(((.(((..........((((((((....))))))))......((((((.(((....))).))))))..)))..)))..)))))))).))))))....)))...)))))). (-35.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGCUGAAUCUUAUUUUAUAAUCUUCUUUCAAAACAAUCAAGUCUUUAAAACUUUUGUUAUAAAGAUGUAAACUAUCACAAUCUUGUGAUAAGAAAUAAGAGUGAAGUUAGGAAAAAUAGUUAUAAGCAGAAAAACAAAUAUUUUUAUGUGCUGAAAAAUCUUGAUACUGGGUCUUUUAUUGCUGAAAUAUUUACUUCUUUUUAUGAUAAAACUGACUUUUGGGCCAGAA (((.(((...(((((((((........................(((((((.(((....))).)))))))......(((((((....))))))).)))))))))..((((((((........((((((((.((((....(((((((((...((..(((((.((((.......)))).)))))..)).)))))))))..)))).))))))))....))))))))..))).))). (-45.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 80 32 77 35 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 250 157 114 37 2 NC_009009:SSA_1328|5end_hypothetical_protein_1344896..1345126_NEGATIVE 246 84 41 57 15 NC_009009:SSA_2107|5end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2111106..2111336_NEGATIVE 237 80 33 68 16 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 235 160 111 131 88 NC_009009:SSA_1007|5end_ABC_transporter_ATP-binding_protein-multiple_sugar_transport,_putative_1008543..1008773_POSITIVE 234 77 31 102 53 NC_009009:SSA_2150|5end_hypothetical_protein_2151116..2151346_NEGATIVE 232 30 1 87 57 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 231 81 57 57 32 NC_009009:SSA_2202|5end_Elongation_factor_Ts,_putative_2203350..2203580_NEGATIVE 231 80 35 73 20 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 227 140 101 102 60 NC_009009:SSA_1298|5end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1315291..1315521_POSITIVE 227 161 123 175 136 NC_009009:SSA_0857|5end_hypothetical_protein_844179..844409_POSITIVE 223 19 4 31 16 NC_009009:SSA_2052|5end_Thioredoxin,_putative_2057507..2057737_NEGATIVE 223 168 124 147 98 NC_009009:SSA_0032|5end_Phosphoribosylformylglycinamidine_cyclo-ligase,_putative_37938..38168_POSITIVE 222 168 122 94 47 NC_009009:SSA_1410|5end_DTDP-4-keto-6-deoxyglucose-3,5-epimerase,_putative_1423086..1423316_NEGATIVE 221 150 101 75 22 NC_009009:SSA_0827|5end_Conserved_uncharacterized_cytosolic_protein,_putative_806033..806263_POSITIVE 220 99 53 100 58 NC_009009:SSA_0388|5end_Mismatch_repair_ATPase_(MutS_family),_putative_382474..382704_POSITIVE 219 18 2 64 49 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 215 68 21 60 7 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 215 188 150 158 124 NC_009009:SSA_1042|5end_Xylanase/chitin_deacetylase,_putative_1058474..1058704_NEGATIVE 213 78 31 195 164 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 148 101 132 83 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 259 80 32 49 7 NC_009009:SSA_0220|3end_PTS_system,_mannose-specific_IIB_component,_putative_216422..216572_POSITIVE 236 139 96 151 95 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 235 160 111 109 66 NC_009009:SSA_1006|3end_Dextransucrase,_putative_1008601..1008751_POSITIVE 232 30 1 66 36 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 231 80 35 59 6 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 227 161 123 132 93 NC_009009:SSA_0856|3end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_844216..844366_POSITIVE 226 78 33 93 47 NC_009009:SSA_1922|3end_hypothetical_protein_1911474..1911624_NEGATIVE 223 168 124 87 38 NC_009009:SSA_0031|3end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_37958..38108_POSITIVE 222 168 122 89 42 NC_009009:SSA_1411|3end_Glucose-1-phosphate_thymidylytransferase,_putative_1423091..1423241_NEGATIVE 219 18 2 38 23 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 215 169 122 129 81 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 211 153 116 105 67 NC_009009:SSA_0329|3end_Glycerol_uptake_facilitator/aquaporin_protein,_putative_323815..323965_POSITIVE 209 140 92 118 60 NC_009009:SSA_1756|3end_Conserved_uncharacterized_protein_1743777..1743927_NEGATIVE 209 148 101 83 43 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 206 48 3 88 31 NC_009009:SSA_2080|3end_hypothetical_protein_2084598..2084748_NEGATIVE 206 166 122 145 101 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 206 140 95 114 74 NC_009009:SSA_1634|3end_Heme_utilization/adhesion_exoprotein,_putative_1635602..1635752_NEGATIVE 205 125 95 104 67 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 202 50 4 52 14 NC_009009:SSA_0932|3end_hypothetical_protein_942804..942954_POSITIVE