Origin IGS: accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcagattttttcttttgcttttatttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggacatctcctttcatcagatatgaggaactaaaaaacgaaatgtaatttaaagatatgagtttaacatctaaagttaatcacaacttactcatttagctaaaaactgagctattctaactcaatctcgaaagagtttggtataagttgtataacttcttatacttattatacacccattcattagtagtagcaaataaaagcaaaagaaaaaatctgcttaagcagattccgattttataaatcactttttgaacttttgtctccattgaaggt Mask Tandem Repeat Region ================================================ accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcagattttttcttttgcttttatttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt Find is-nt database================================================ Query_seq: SSA_0909:SSA_0910|SSA_0909:SSA_0910:Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative:ABC-type multidrug transporter, ATPase component, putative:->->:921219..921495 277 accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcagattttttcttttgcttttatttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0909:SSA_0910|SSA_0909:SSA_0910:Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative:ABC-type multidrug transporter, ATPase component, putative:->->:921219..921495 277 accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcagattttttcttttgcttttatttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0909:SSA_0910|SSA_0909:SSA_0910:Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative:ABC-type multidrug transporter, ATPase component, putative:->->:921219..921495 277 accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcagattttttcttttgcttttatttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcagattttttcttttgcttttatttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 8 End: 157 ....... M E T K V Q K V I Y K I G I C L S R F F L L L L F A T T N E W V Y N K Y K K L Y N L Y Q T L S R L S ........................................................................................................................ Protein_Len: 31 Strand: - Start: 37 End: 129 .................................... L I P I Q K L L N K R K S K N A V V L S H T Y L L Y L F N Y M .................................................................................................................................................... accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcagattttttcttttgcttttatttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt 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: 86 Start: 80 End: 109 ...............................................................................TTTGCTACTACTAATGAATGGGTGTATAAT........................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 111 End: 140 ..............................................................................................................TTTGGTATAAGTTGTATAACTTCTTATACT......................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcagattttttcttttgcttttatttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -6.7 Tail_Score: -5.85244 Start: 48 End: 61 Full_Region: TTTATAAAATCGGAA TCTGC TTAA GCAGA TTTTTTCTTTTGCTT ...............................................TCTGCTTAAGCAGA........................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_0909:SSA_0910|SSA_0909:SSA_0910:Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative:ABC-type multidrug transporter, ATPase component, putative:->->:921219..921495 277 accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcagattttttcttttgcttttatttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt Intra-Species Hit: Count: 1 Min: 1 Max: 277 Len: 277 Subject: NC_009009_SSA_0909_SSA_0910|Transcriptional regulator, AbrB family (stationary/sporulation gene expression), putative:ABC-type multidrug transporter, ATPase component, putative|POSITIVE:POSITIVE|[921219,921495]|277 HSP 1 e-value: 1.0E-109 bit: 394.0 Len: 199 Query Start:79 Query End:277 Subject Strand: POSITIVE Subject Start: 79 Subject End: 277 ..............................................................................atttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt ..............................................................................atttgctactactaatgaatgggtgtataataagtataagaagttatacaacttataccaaactctttcgagattgagttagaatagctcagtttttagctaaatgagtaagttgtgattaactttagatgttaaactcatatctttaaattacatttcgttttttagttcctcatatctgatgaaaggagatgtcctt HSP 2 e-value: 1.0E-26 bit: 121.0 Len: 61 Query Start:1 Query End:61 Subject Strand: POSITIVE Subject Start: 1 Subject End: 61 accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcaga........................................................................................................................................................................................................................ accttcaatggagacaaaagttcaaaaagtgatttataaaatcggaatctgcttaagcaga........................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUCAAUGGAGACAAAAGUUCAAAAAGUGAUUUAUAAAAUCGGAAUCUGCUUAAGCAGAUUUUUUCUUUUGCUUUUAUUUGCUACUACUAAUGAAUGGGUGUAUAAUAAGUAUAAGAAGUUAUACAACUUAUACCAAACUCUUUCGAGAUUGAGUUAGAAUAGCUCAGUUUUUAGCUAAAUGAGUAAGUUGUGAUUAACUUUAGAUGUUAAACUCAUAUCUUUAAAUUACAUUUCGUUUUUUAGUUCCUCAUAUCUGAUGAAAGGAGAUGUCCUU .((......)).((((..(((...((((((((((.....)))).((((((((....))))))))........))))))....)))...(((((.(((((((((((............(((((((((((((((((........((...((((((((((((...)))))))))))).))........))))))))))..))))))).(((((.......))))).......)))).))))))).)))))(((((((.....))))..)))..))))... (-57.99) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGACAUCUCCUUUCAUCAGAUAUGAGGAACUAAAAAACGAAAUGUAAUUUAAAGAUAUGAGUUUAACAUCUAAAGUUAAUCACAACUUACUCAUUUAGCUAAAAACUGAGCUAUUCUAACUCAAUCUCGAAAGAGUUUGGUAUAAGUUGUAUAACUUCUUAUACUUAUUAUACACCCAUUCAUUAGUAGUAGCAAAUAAAAGCAAAAGAAAAAAUCUGCUUAAGCAGAUUCCGAUUUUAUAAAUCACUUUUUGAACUUUUGUCUCCAUUGAAGGU ...........((((((..(((((.(((..........................((..(((((((((((.......))))).........))))))....)).........((((((((((..(((.(((....))).)))((((((...((((((....))))))...)))))).........)))).)))))).........((((((....(((((((....)))))))..((((.....))))..))))))..))).)))))....)))))). (-52.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 189 142 157 104 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 289 83 43 179 128 NC_009009:SSA_1521|5end_Phosphoenolpyruvate_carboxylase,_putative_1530683..1530913_NEGATIVE 284 198 152 183 137 NC_009009:SSA_1618|5end_hypothetical_protein_1621574..1621804_NEGATIVE 281 178 135 148 109 NC_009009:SSA_1638|5end_hypothetical_protein_1641325..1641555_NEGATIVE 271 84 42 158 119 NC_009009:SSA_0651|5end_hypothetical_protein_634548..634778_POSITIVE 270 61 25 72 34 NC_009009:SSA_2127|5end_hypothetical_protein_2130850..2131080_NEGATIVE 270 61 25 167 129 NC_009009:SSA_2126|5end_hypothetical_protein_2130755..2130985_NEGATIVE 255 185 142 62 9 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 249 179 137 144 96 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 247 190 142 128 69 NC_009009:SSA_0741|5end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_723773..724003_POSITIVE 244 190 141 141 99 NC_009009:SSA_1147|5end_Beta-glucosides_PTS,_EIIB,_putative_1176782..1177012_POSITIVE 242 168 130 151 104 NC_009009:SSA_0145|5end_Transcriptional_regulator,_TetR_family,_putative_139380..139610_NEGATIVE 240 82 47 106 62 NC_009009:SSA_0138|5end_Metal-binding_(Zn)_permease,_putative_132533..132763_POSITIVE 238 180 141 198 149 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 235 74 33 207 168 NC_009009:SSA_0842|5end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827330..827560_POSITIVE 234 100 51 181 128 NC_009009:SSA_0868|5end_hypothetical_protein_861535..861765_NEGATIVE 234 88 41 67 12 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 230 88 48 92 46 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 230 195 163 162 123 NC_009009:SSA_0121|5end_hypothetical_protein_115183..115413_POSITIVE 229 179 146 41 1 NC_009009:SSA_0437|5end_30S_ribosomal_protein_S6,_putative_440313..440543_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 83 43 132 81 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 284 198 152 78 32 NC_009009:SSA_1619|3end_Ribosome_recycling_factor,_putative_1621679..1621829_NEGATIVE 281 178 135 134 95 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE 276 78 36 75 31 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 272 86 47 127 86 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 271 84 42 134 95 NC_009009:SSA_0650|3end_GTP-binding_protein_TypA/BipA,_putative_634604..634754_POSITIVE 270 61 25 71 33 NC_009009:SSA_2128|3end_hypothetical_protein_2130851..2131001_NEGATIVE 269 194 156 139 105 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE 264 187 141 100 51 NC_009009:SSA_1615|3end_Alanine_dehydrogenase,_putative_1619318..1619468_POSITIVE 249 179 137 151 103 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 248 174 144 83 51 NC_009009:SSA_0998|3end_hypothetical_protein_998758..998908_POSITIVE 248 82 43 86 38 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 247 190 142 106 47 NC_009009:SSA_0740|3end_C4-dicarboxylate_anaerobic_carrier,_possible_arginine_transporter,_putative_723831..723981_POSITIVE 245 169 136 34 1 NC_009009:SSA_0860|3end_N-acetylmuramidase/lysin,_putative_851738..851888_POSITIVE 244 190 141 144 102 NC_009009:SSA_1146|3end_Phosphotransferase_system_cellobiose-specific_component_IIA,_putative_1176865..1177015_POSITIVE 240 82 47 96 52 NC_009009:SSA_0137|3end_ABC_transporter_(permease),_Zn_porter,_putative_132603..132753_POSITIVE 237 249 201 116 68 NC_009009:SSA_2141|3end_Argininosuccinate_lyase,_putative_2140819..2140969_NEGATIVE 234 88 41 104 49 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 233 176 136 110 64 NC_009009:SSA_1981|3end_hypothetical_protein_1974759..1974909_NEGATIVE 233 74 43 33 2 NC_009009:SSA_0841|3end_hypothetical_protein_827236..827386_POSITIVE