Origin IGS: tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga .........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 tctattcctctttatttttaaaattacaaattaaaaaccgcaaacttctccaaaaaggacgaaaattcgcggtaccacctttgtttaggcaagacgatagcatgatgctcctcttgcccctctttgtccgtaacgtggaccaccgtctcatcctactggtttcagacgaaagttctgtaaaatgatagcccaagcaagatggactgcagatctctcaccatcatctgctcgctgaaagtattttgcttggtctgtgtttttacaatcttatcttctttaaaaa Mask Tandem Repeat Region ================================================ tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga Find is-nt database================================================ Query_seq: SSA_0660:SSA_0661|SSA_0660:SSA_0661:Cell division protein DivIVA, putative:Isoleucyl-tRNA synthetase, putative:->->:644733..645015 283 tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0660:SSA_0661|SSA_0660:SSA_0661:Cell division protein DivIVA, putative:Isoleucyl-tRNA synthetase, putative:->->:644733..645015 283 tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0660:SSA_0661|SSA_0660:SSA_0661:Cell division protein DivIVA, putative:Isoleucyl-tRNA synthetase, putative:->->:644733..645015 283 tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 18 End: 119 ................. M V K T Q T K Q N T F S E Q M M V R D L Q S I L L G L S F Y R T F V .................................................................................................................................................................... Protein_Len: 39 Strand: + Start: 141 End: 257 ............................................................................................................................................ M V H V T D K E G Q E E H H A I V L P K Q R W Y R E F S S F L E K F A V F N L .......................... Protein_Len: 60 Strand: + Start: 73 End: 279 ........................................................................ M C S P S C L G Y H F T E L S S E T S R M R R W S T L R T K R G K R S I M L S S C L N K G G T A N F R P F W R S L R F L .... Protein_Len: 51 Strand: - Start: 102 End: 254 ..................................................................................................... K V S S E D S V L L I L R H D V N R V F L P L L L M M S D D Q R F L P P V A F K R G K Q L L K R N K M ............................. tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -3.0 Tail_Score: -5.05505 Start: 212 End: 246 Full_Region: TAAACAAAGGTGGTA CCGCGAATTTTCGTCC TTTTT GGAGAAGTTTGCGG TTTTTAATTTGTAAT ...................................................................................................................................................................................................................CCGCGAATTTTCGTCCTTTTTGGAGAAGTTTGCGG..................................... Find igs database================================================ Query_seq: SSA_0660:SSA_0661|SSA_0660:SSA_0661:Cell division protein DivIVA, putative:Isoleucyl-tRNA synthetase, putative:->->:644733..645015 283 tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga Intra-Species Hit: Count: 1 Min: 1 Max: 283 Len: 283 Subject: NC_009009_SSA_0660_SSA_0661|Cell division protein DivIVA, putative:Isoleucyl-tRNA synthetase, putative|POSITIVE:POSITIVE|[644733,645015]|283 HSP 1 e-value: 1.0E-159 bit: 561.0 Len: 283 Query Start:1 Query End:283 Subject Strand: POSITIVE Subject Start: 1 Subject End: 283 tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga tttttaaagaagataagattgtaaaaacacagaccaagcaaaatactttcagcgagcagatgatggtgagagatctgcagtccatcttgcttgggctatcattttacagaactttcgtctgaaaccagtaggatgagacggtggtccacgttacggacaaagaggggcaagaggagcatcatgctatcgtcttgcctaaacaaaggtggtaccgcgaattttcgtcctttttggagaagtttgcggtttttaatttgtaattttaaaaataaagaggaataga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAAAGAAGAUAAGAUUGUAAAAACACAGACCAAGCAAAAUACUUUCAGCGAGCAGAUGAUGGUGAGAGAUCUGCAGUCCAUCUUGCUUGGGCUAUCAUUUUACAGAACUUUCGUCUGAAACCAGUAGGAUGAGACGGUGGUCCACGUUACGGACAAAGAGGGGCAAGAGGAGCAUCAUGCUAUCGUCUUGCCUAAACAAAGGUGGUACCGCGAAUUUUCGUCCUUUUUGGAGAAGUUUGCGGUUUUUAAUUUGUAAUUUUAAAAAUAAAGAGGAAUAGA (((((((((.........((((((((....((.((((((((.(((((........((((((...........)))))))))..)).)))))))).))....))))))))..((((.(((((.(((..((.((((.(.....).))))))))).)))))))))..((((((((.((((.....))..)).))))))))..(((((......((((((((((((..(((.....)))))))))))))))......)))))..))))))))).............. (-76.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUUCCUCUUUAUUUUUAAAAUUACAAAUUAAAAACCGCAAACUUCUCCAAAAAGGACGAAAAUUCGCGGUACCACCUUUGUUUAGGCAAGACGAUAGCAUGAUGCUCCUCUUGCCCCUCUUUGUCCGUAACGUGGACCACCGUCUCAUCCUACUGGUUUCAGACGAAAGUUCUGUAAAAUGAUAGCCCAAGCAAGAUGGACUGCAGAUCUCUCACCAUCAUCUGCUCGCUGAAAGUAUUUUGCUUGGUCUGUGUUUUUACAAUCUUAUCUUCUUUAAAAA ..............((((((((...(((((......(((((((..((((((.....))).)))..)).)))))......)))))...(((((((.((..((.....)))).))))))).......(((((.....)))))...(((((...((....))....))))).(((...(((((((..((((.(((((((((((((...((((((...........))))))...))......))))))))))).))))..)))))))..)))......)))))))) (-69.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 216 173 58 7 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 362 116 75 219 184 NC_009009:SSA_1183|5end_hypothetical_protein_1211453..1211683_NEGATIVE 358 89 52 226 185 NC_009009:SSA_0366|5end_hypothetical_protein_357506..357736_POSITIVE 349 210 162 197 151 NC_009009:SSA_0504|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503009..503239_POSITIVE 349 163 123 64 26 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 345 179 134 227 178 NC_009009:SSA_0061|5end_Tagatose_1,6-diphosphate_aldolase,_putative_62670..62900_POSITIVE 342 98 51 231 174 NC_009009:SSA_1164|5end_hypothetical_protein_1191138..1191368_NEGATIVE 339 129 81 59 6 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 338 108 61 76 10 NC_009009:SSA_1101|5end_Multidrug_resistance_efflux_pump/hemolysin_secretion_transmembrane_protein,_putative_1121911..1122141_POSITIVE 331 182 146 73 36 NC_009009:SSA_1909|5end_Transcriptional_attenuator_LytR,_putative_1902142..1902372_NEGATIVE 330 246 201 213 168 NC_009009:SSA_0054|5end_Phosphotransferase_system_sugar-specific_EIIB_component,_putative_58532..58762_POSITIVE 329 196 166 49 16 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 329 180 136 97 50 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 326 197 169 197 159 NC_009009:SSA_0532|5end_Propanediol_utilization_protein_PduB,_putative_528244..528474_POSITIVE 325 95 52 46 3 NC_009009:SSA_1276|5end_Conserved_uncharacterized_protein_1298446..1298676_NEGATIVE 322 107 64 231 173 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 320 176 132 64 12 NC_009009:SSA_0055|5end_PTS_system,_IIC_component,_putative_59034..59264_POSITIVE 317 217 172 191 140 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 314 208 161 51 9 NC_009009:SSA_1428|5end_hypothetical_protein_1436348..1436578_NEGATIVE 313 69 28 218 174 NC_009009:SSA_0701|5end_Cation_transporter_CorA_family,_putative_684368..684598_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 215 173 132 78 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 331 182 146 64 27 NC_009009:SSA_1910|3end_hypothetical_protein_1902151..1902301_NEGATIVE 323 189 148 95 45 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 321 177 133 73 20 NC_009009:SSA_1930|3end_Acetyl-CoA_carboxylase_alpha_subunit,_putative_1917777..1917927_NEGATIVE 316 251 211 53 12 NC_009009:SSA_0503|3end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503102..503252_POSITIVE 314 208 161 44 2 NC_009009:SSA_1429|3end_hypothetical_protein_1436355..1436505_NEGATIVE 308 177 131 70 16 NC_009009:SSA_1773|3end_hypothetical_protein_1759535..1759685_NEGATIVE 305 183 144 118 77 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 305 157 113 149 105 NC_009009:SSA_0788|3end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_772523..772673_POSITIVE 300 97 51 122 66 NC_009009:SSA_1383|3end_Aspartate_aminotransferase,_putative_1400537..1400687_NEGATIVE 300 96 51 142 102 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 300 180 133 66 21 NC_009009:SSA_0562|3end_hypothetical_protein_554859..555009_POSITIVE 299 94 51 84 26 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 298 97 52 127 74 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 298 90 45 135 88 NC_009009:SSA_1587|3end_hypothetical_protein_1588238..1588388_NEGATIVE 297 101 75 151 125 NC_009009:SSA_1184|3end_DNA_topoisomerase_I,_putative_1211512..1211662_NEGATIVE 297 175 131 72 23 NC_009009:SSA_0896|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_888441..888591_POSITIVE 294 97 51 47 9 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 292 100 66 70 39 NC_009009:SSA_0316|3end_hypothetical_protein_311342..311492_POSITIVE 291 229 183 144 90 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE