Origin IGS: tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca .........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 tgtttgtttctccttttagtttgtgaattcgattcaatttgatgattttcatcaactttaacagtataacaaaacttttttgtaaagtaaagttacttgacagatttttttcttctttttgaaaaacccctgagcttctagttgtcttctttttgcttgataggaaaaagtttcaaatccgcctctatattttcccaatcttctgaaaatttaaaaattttcttctgtaaaatacagcctaagtgtggtataataaagcacaaagattactgta Mask Tandem Repeat Region ================================================ tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca Find is-nt database================================================ Query_seq: SSA_2286:SSA_2287|SSA_2286:SSA_2287:Dihydroxy-acid dehydratase, putative:50S ribosomal protein L32, putative:<-->:2289687..2289960 274 tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2286:SSA_2287|SSA_2286:SSA_2287:Dihydroxy-acid dehydratase, putative:50S ribosomal protein L32, putative:<-->:2289687..2289960 274 tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2286:SSA_2287|SSA_2286:SSA_2287:Dihydroxy-acid dehydratase, putative:50S ribosomal protein L32, putative:<-->:2289687..2289960 274 tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 12 End: 134 ........... M C F I I P H L G C I L Q K K I F K F S E D W E N I E A D L K L F P I K Q K E D N ............................................................................................................................................ Protein_Len: 50 Strand: + Start: 65 End: 214 ................................................................ M F R R L G K Y R G G F E T F S Y Q A K R R Q L E A Q G F F K K K K K I C Q V T L L Y K K V L L Y C ............................................................ Protein_Len: 34 Strand: + Start: 172 End: 273 ........................................................................................................................................................................... M S S N F T L Q K S F V I L L K L M K I I K L N R I H K L K G E T N . Protein_Len: 31 Strand: - Start: 156 End: 248 ........................................................................................................................................................... F S S F F R D L L K V K C F L K T I S N F N I F I M L N F R M .......................... Protein_Len: 44 Strand: - Start: 2 End: 133 . C Y D K H K I I G C K P Q I K C F F I K L N E S S Q S F I S A S K F S K G I L C F S S M ............................................................................................................................................. tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca 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: 83 Start: 183 End: 212 ......................................................................................................................................................................................CTTTACTTTACAAAAAAGTTTTGTTATACT.............................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 21 End: 50 ....................CTGTAAAATACAGCCTAAGTGTGGTATAAT................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 91 HP_score: -4.1 Tail_Score: -6.04419 Start: 171 End: 196 Full_Region: gtataacaaaacttt tttgtaaagta aagt tacttgacaga tttttttcttctttt ..........................................................................................................................................................................tttgtaaagtaaagttacttgacaga.............................................................................. Find igs database================================================ Query_seq: SSA_2286:SSA_2287|SSA_2286:SSA_2287:Dihydroxy-acid dehydratase, putative:50S ribosomal protein L32, putative:<-->:2289687..2289960 274 tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 274 Len: 274 Subject: NC_009009_SSA_2286_SSA_2287|Dihydroxy-acid dehydratase, putative:50S ribosomal protein L32, putative|NEGATIVE:POSITIVE|[2289687,2289960]|274 HSP 1 e-value: 1.0E-141 bit: 502.0 Len: 274 Query Start:1 Query End:274 Subject Strand: POSITIVE Subject Start: 1 Subject End: 274 tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagnnnnnnntctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca tacagtaatctttgtgctttattataccacacttaggctgtattttacagaagaaaatttttaaattttcagaagattgggaaaatatagaggcggatttgaaactttttcctatcaagcaaaaagaagacaactagaagctcaggggtttttcaaaaagaagaaaaaaatctgtcaagtaactttactttacaaaaaagttttgttatactgttaaagttgatgaaaatcatcaaattgaatcgaattcacaaactaaaaggagaaacaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAGUAAUCUUUGUGCUUUAUUAUACCACACUUAGGCUGUAUUUUACAGAAGAAAAUUUUUAAAUUUUCAGAAGAUUGGGAAAAUAUAGAGGCGGAUUUGAAACUUUUUCCUAUCAAGCAAAAAGAAGACAACUAGAAGCUCAGGGGUUUUUCAAAAAGAAGAAAAAAAUCUGUCAAGUAACUUUACUUUACAAAAAAGUUUUGUUAUACUGUUAAAGUUGAUGAAAAUCAUCAAAUUGAAUCGAAUUCACAAACUAAAAGGAGAAACAAACA ....((..(((((...((((((....(((..(((...(((((...)))))..(((((((....)))))))..)))..)))......))))))..((((((((..((((((.((....)).))))))..((((..........((((..((((((........))))))..))))....(((((...(((((.....)))))...)))))..))))....((((((.....))))))......)))))))).........)))))...))..... (-49.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUGUUUCUCCUUUUAGUUUGUGAAUUCGAUUCAAUUUGAUGAUUUUCAUCAACUUUAACAGUAUAACAAAACUUUUUUGUAAAGUAAAGUUACUUGACAGAUUUUUUUCUUCUUUUUGAAAAACCCCUGAGCUUCUAGUUGUCUUCUUUUUGCUUGAUAGGAAAAAGUUUCAAAUCCGCCUCUAUAUUUUCCCAAUCUUCUGAAAAUUUAAAAAUUUUCUUCUGUAAAAUACAGCCUAAGUGUGGUAUAAUAAAGCACAAAGAUUACUGUA .................((((.(((((.((((......)))).....))))).))))...((((((..((((......(((((.(((((....))))).)))))..((((((........))))))...............))))..(((((.(((((....(((............)))....((((((((............(((((((....)))))))..(((((...)))))...)))))))).......))))).))))).)))))). (-42.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 827 120 71 211 162 NC_009009:SSA_2286|5end_Dihydroxy-acid_dehydratase,_putative_2289596..2289826_NEGATIVE 278 55 21 156 122 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 261 151 117 199 156 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 259 156 115 223 176 NC_009009:SSA_2081|5end_hypothetical_protein_2085309..2085539_POSITIVE 254 149 104 71 21 NC_009009:SSA_1729|5end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1715699..1715929_NEGATIVE 252 53 15 159 121 NC_009009:SSA_1748|5end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1734478..1734708_NEGATIVE 251 166 125 197 151 NC_009009:SSA_1666|5end_Collagen-binding_surface_protein,_putative_1667312..1667542_NEGATIVE 247 113 71 88 52 NC_009009:SSA_1525|5end_Lyzozyme_M1_(1,4-beta-N-acetylmuramidase),_putative_1532746..1532976_POSITIVE 245 121 91 164 132 NC_009009:SSA_0284|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIC_component,_putative_274888..275118_POSITIVE 243 147 105 184 140 NC_009009:SSA_0311|5end_hypothetical_protein_305877..306107_POSITIVE 242 47 9 141 105 NC_009009:SSA_0871|5end_Cell_division_protein_FtsX,_putative_863621..863851_POSITIVE 241 118 76 75 33 NC_009009:SSA_1775|5end_Potassium_uptake_protein,_Trk_family,_putative_1761284..1761514_POSITIVE 240 117 74 157 106 NC_009009:SSA_2006|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme,_putative_2007215..2007445_NEGATIVE 239 149 105 85 35 NC_009009:SSA_0211|5end_hypothetical_protein_208041..208271_POSITIVE 236 151 117 98 61 NC_009009:SSA_1568|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571200..1571430_POSITIVE 235 175 144 189 158 NC_009009:SSA_2284|5end_Histidyl-tRNA_synthetase,_putative_2287272..2287502_NEGATIVE 235 143 105 138 98 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 234 50 5 220 181 NC_009009:SSA_0106|5end_30S_ribosomal_protein_S10,_putative_107772..108002_POSITIVE 227 135 92 209 172 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 227 179 131 164 117 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 148 108 72 30 NC_009009:SSA_1327|3end_hypothetical_protein_1343750..1343900_NEGATIVE 261 151 117 86 43 NC_009009:SSA_0814|3end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_795519..795669_NEGATIVE 254 163 124 64 13 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 245 121 91 146 114 NC_009009:SSA_0283|3end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274950..275100_POSITIVE 242 47 9 148 112 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 239 149 105 88 38 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 236 151 117 85 48 NC_009009:SSA_1567|3end_Polar_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_1571267..1571417_POSITIVE 236 137 91 75 30 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 235 143 105 46 6 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 234 148 105 82 33 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 229 145 105 149 103 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 229 118 77 45 3 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 226 59 13 66 28 NC_009009:SSA_1225|3end_Branched-chain_amino_acid_aminotransferase,_putative_1247589..1247739_NEGATIVE 226 153 136 87 70 NC_009009:SSA_0362|3end_Thioredoxin,_putative_353594..353744_POSITIVE 225 130 81 60 6 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 220 177 134 89 42 NC_009009:SSA_2128|3end_hypothetical_protein_2130851..2131001_NEGATIVE 220 153 112 92 44 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 214 146 105 100 52 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 214 138 91 85 42 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 214 177 139 49 14 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE