Origin IGS: taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt .........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 aaatgaagtattcgcgcgagtggatactttttttaaaatattttttgaaaccgcttgcaactctaaagagaatagtgtatactataacagtagaaaagtgaaacggttaaccataaattaaagcattattttataagggaaacgtagttcacttttattttttgaaaataagttaaccgcttcgcccagagtttgaaaataatttcgcagtgaaaggttgattgctcgtctagaaaggagaccta Mask Tandem Repeat Region ================================================ taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt Find is-nt database================================================ Query_seq: SSA_2086:SSA_2087|SSA_2086:SSA_2087:hypothetical protein:Conserved uncharacterized protein:<-<-:2091519..2091763 245 taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2086:SSA_2087|SSA_2086:SSA_2087:hypothetical protein:Conserved uncharacterized protein:<-<-:2091519..2091763 245 taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2086:SSA_2087|SSA_2086:SSA_2087:hypothetical protein:Conserved uncharacterized protein:<-<-:2091519..2091763 245 taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 24 End: 125 ....................... M N L S L R N Y F Q T L G E A V N L F S K N K S E L R F P Y K I M L ........................................................................................................................ Protein_Len: 32 Strand: - Start: 148 End: 243 ................................................................................................................................................... K E V T I T Y V I R K L T A L P K L F Y K L F L I W E R S Y K M .. Protein_Len: 33 Strand: - Start: 128 End: 226 ............................................................................................................................... N I T L R K V K R S N Y Y V S N E K S N C A T E F F I K F F T D M ................... taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt 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: 163 End: 192 ..................................................................................................................................................................CTTGCAACTCTAAAGAGAATAGTGTATACT..................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2086:SSA_2087|SSA_2086:SSA_2087:hypothetical protein:Conserved uncharacterized protein:<-<-:2091519..2091763 245 taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: NC_009009_SSA_2086_SSA_2087|hypothetical protein:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2091519,2091763]|245 HSP 1 e-value: 1.0E-124 bit: 444.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttnnnnnnngtatccactcgcgcgaatacttcattt taggtctcctttctagacgagcaatcaacctttcactgcgaaattattttcaaactctgggcgaagcggttaacttattttcaaaaaataaaagtgaactacgtttcccttataaaataatgctttaatttatggttaaccgtttcacttttctactgttatagtatacactattctctttagagttgcaagcggtttcaaaaaatattttaaaaaaagtatccactcgcgcgaatacttcattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUCUCCUUUCUAGACGAGCAAUCAACCUUUCACUGCGAAAUUAUUUUCAAACUCUGGGCGAAGCGGUUAACUUAUUUUCAAAAAAUAAAAGUGAACUACGUUUCCCUUAUAAAAUAAUGCUUUAAUUUAUGGUUAACCGUUUCACUUUUCUACUGUUAUAGUAUACACUAUUCUCUUUAGAGUUGCAAGCGGUUUCAAAAAAUAUUUUAAAAAAAGUAUCCACUCGCGCGAAUACUUCAUUU ((((.......))))..((.((.................(((((..(((...((((((((..((((((((((((..................((....))..........((((((.(((....))).))))))))))))))))))..............(((((....))))).....))))))))..)))..))))).....(((((((....)))))))......)).))............ (-40.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGAAGUAUUCGCGCGAGUGGAUACUUUUUUUAAAAUAUUUUUUGAAACCGCUUGCAACUCUAAAGAGAAUAGUGUAUACUAUAACAGUAGAAAAGUGAAACGGUUAACCAUAAAUUAAAGCAUUAUUUUAUAAGGGAAACGUAGUUCACUUUUAUUUUUUGAAAAUAAGUUAACCGCUUCGCCCAGAGUUUGAAAAUAAUUUCGCAGUGAAAGGUUGAUUGCUCGUCUAGAAAGGAGACCUA ......(((((.(((((((((((.......((((((((....))))))))))))))))..(((....)))....))).)))))....(((...(((((((((...(((..(((((((.(((....))).)))))..))..)))....))))))))).....)))......((((((((..(((((...(((............)))...))))).))))))))....((((.......))))... (-52.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 912 70 21 161 112 NC_009009:SSA_2086|5end_hypothetical_protein_2091428..2091658_NEGATIVE 355 203 162 179 138 NC_009009:SSA_1593|5end_Dipeptidase,_putative_1598054..1598284_NEGATIVE 317 42 14 206 173 NC_009009:SSA_1613|5end_hypothetical_protein_1616975..1617205_NEGATIVE 291 178 133 75 28 NC_009009:SSA_1502|5end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1506219..1506449_NEGATIVE 275 190 141 119 62 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 274 70 21 230 192 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 273 200 154 183 136 NC_009009:SSA_1591|5end_Dipeptidase,_putative_1595451..1595681_NEGATIVE 273 39 7 142 101 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 273 37 3 129 92 NC_009009:SSA_0419|5end_Alpha-galactosidase,_putative_416213..416443_POSITIVE 270 69 29 173 128 NC_009009:SSA_1176|5end_Acetoin_dehydrogenase,_E1_component,_beta_subunit,_putative_1205405..1205635_NEGATIVE 266 41 6 132 98 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 264 69 32 52 12 NC_009009:SSA_1084|5end_Conserved_uncharacterized_protein_1101675..1101905_POSITIVE 264 70 28 230 186 NC_009009:SSA_0167|5end_Hypothetical_protein_(Asparagine/proline-rich)_165254..165484_POSITIVE 263 39 1 55 14 NC_009009:SSA_1053|5end_Pyruvate_phosphate_dikinase,_putative_1070068..1070298_NEGATIVE 260 70 21 177 129 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 258 70 22 65 4 NC_009009:SSA_1238|5end_hypothetical_protein_1263154..1263384_NEGATIVE 257 76 35 171 128 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 253 60 11 149 110 NC_009009:SSA_1936|5end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923838..1924068_NEGATIVE 253 72 36 164 121 NC_009009:SSA_1073|5end_Gamma-glutamyl_phosphate_reductase,_putative_1090886..1091116_POSITIVE 253 199 157 195 140 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 49 4 115 70 NC_009009:SSA_1594|3end_Metalloendopeptidase,_putative_1598457..1598607_NEGATIVE 275 190 141 73 16 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 273 200 154 58 11 NC_009009:SSA_1592|3end_hypothetical_protein_1595576..1595726_NEGATIVE 273 39 7 108 67 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 270 69 29 129 84 NC_009009:SSA_1178|3end_Acetoin_dehydrogenase,_E1_component,_alpha_subunit,_putative_1205449..1205599_NEGATIVE 268 190 141 145 74 NC_009009:SSA_1312|3end_RADC-like_protein,_putative_1328737..1328887_NEGATIVE 264 69 32 49 9 NC_009009:SSA_1083|3end_Conserved_uncharacterized_protein_1101752..1101902_POSITIVE 260 70 21 135 87 NC_009009:SSA_2012|3end_hypothetical_protein_2012898..2013048_NEGATIVE 258 70 22 68 7 NC_009009:SSA_1239|3end_hypothetical_protein_1263151..1263301_NEGATIVE 253 60 11 136 97 NC_009009:SSA_1937|3end_Malonyl-CoA:ACP_transacylase,_putative_1923851..1924001_NEGATIVE 253 72 36 142 99 NC_009009:SSA_1072|3end_Glutamate_5-kinase,_putative_1090944..1091094_POSITIVE 250 80 32 131 88 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 249 70 28 141 97 NC_009009:SSA_2106|3end_Flavin_monoxygenase,_putative_2108015..2108165_NEGATIVE 248 199 151 114 59 NC_009009:SSA_1658|3end_Cationic_amino_acid_transporter,_putative_1653274..1653424_NEGATIVE 247 45 2 131 88 NC_009009:SSA_1753|3end_Transcriptional_regulator,_GntR_family_(repressor_of_trehalose_operon),_putative_1742740..1742890_POSITIVE 245 83 47 101 54 NC_009009:SSA_1471|3end_hypothetical_protein_1476981..1477131_NEGATIVE 245 70 29 146 105 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 243 35 1 127 92 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 243 180 139 62 18 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 242 70 25 135 91 NC_009009:SSA_1645|3end_hypothetical_protein_1645601..1645751_NEGATIVE