Origin IGS: gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc .........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 gatgacagttctcaatcggaatgattgagagcttttttatataggtggcttttaaaagtcaagcagtctagccttgcgtttctctcattcttgggaatactgtgtttttctgaaagaactgttgaaaaagccattttctctgtttcattttaatttcaattgtcttatttatctaaaagtataggaaatttcccgaatctgtggtataataaatggcaataccttgaaagagctttattttaaac Mask Tandem Repeat Region ================================================ gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc Find is-nt database================================================ Query_seq: SSA_1494:SSA_1495|SSA_1494:SSA_1495:Conserved uncharacterized protein:S-adenosylmethionine synthetase, putative:<-<-:1500864..1501108 245 gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1494:SSA_1495|SSA_1494:SSA_1495:Conserved uncharacterized protein:S-adenosylmethionine synthetase, putative:<-<-:1500864..1501108 245 gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1494:SSA_1495|SSA_1494:SSA_1495:Conserved uncharacterized protein:S-adenosylmethionine synthetase, putative:<-<-:1500864..1501108 245 gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 74 End: 175 ......................................................................... M N K T I E I K M K Q R K W L F Q Q F F Q K N T V F P R M R E T Q G ...................................................................... Protein_Len: 40 Strand: + Start: 112 End: 231 ............................................................................................................... M A F S T V L S E K H S I P K N E R N A R L D C L T F K S H L Y K K A L N H S D .............. Protein_Len: 42 Strand: - Start: 96 End: 221 ............................................................................................... F S V S F I A K E V T R E S F C L I G L F S L F A L S S Q K V K L L W R Y L F A R M ........................ Protein_Len: 36 Strand: - Start: 65 End: 172 ................................................................ V K L Y I L C N F N F H F L S F P K K L L E K L F V C Y E W S H S F R M ......................................................................... gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc 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: 36 End: 65 ...................................ATAGGAAATTTCCCGAATCTGTGGTATAAT.................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 70 End: 99 .....................................................................TTAGATAAATAAGACAATTGAAATTAAAAT.................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 48 HP_score: -2.9 Tail_Score: -3.41795 Start: 108 End: 122 Full_Region: tctgaaagaactgtt gaaaa agcca ttttc tctgtttcattttaa ...........................................................................................................gaaaaagccattttc........................................................................................................................... Find igs database================================================ Query_seq: SSA_1494:SSA_1495|SSA_1494:SSA_1495:Conserved uncharacterized protein:S-adenosylmethionine synthetase, putative:<-<-:1500864..1501108 245 gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: NC_009009_SSA_1494_SSA_1495|Conserved uncharacterized protein:S-adenosylmethionine synthetase, putative|NEGATIVE:NEGATIVE|[1500864,1501108]|245 HSP 1 e-value: 1.0E-136 bit: 486.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc gtttaaaataaagctctttcaaggtattgccatttattataccacagattcgggaaatttcctatacttttagataaataagacaattgaaattaaaatgaaacagagaaaatggctttttcaacagttctttcagaaaaacacagtattcccaagaatgagagaaacgcaaggctagactgcttgacttttaaaagccacctatataaaaaagctctcaatcattccgattgagaactgtcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUAAAAUAAAGCUCUUUCAAGGUAUUGCCAUUUAUUAUACCACAGAUUCGGGAAAUUUCCUAUACUUUUAGAUAAAUAAGACAAUUGAAAUUAAAAUGAAACAGAGAAAAUGGCUUUUUCAACAGUUCUUUCAGAAAAACACAGUAUUCCCAAGAAUGAGAGAAACGCAAGGCUAGACUGCUUGACUUUUAAAAGCCACCUAUAUAAAAAAGCUCUCAAUCAUUCCGAUUGAGAACUGUCAUC ((((((((..............(((((...........)))))........((((....))))....))))))))......((((...........................(((((((((((((((((((((((.......................)))))))..(....).....)))).)))).....))))))))...............((((((((.....))))))))..))))... (-44.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGACAGUUCUCAAUCGGAAUGAUUGAGAGCUUUUUUAUAUAGGUGGCUUUUAAAAGUCAAGCAGUCUAGCCUUGCGUUUCUCUCAUUCUUGGGAAUACUGUGUUUUUCUGAAAGAACUGUUGAAAAAGCCAUUUUCUCUGUUUCAUUUUAAUUUCAAUUGUCUUAUUUAUCUAAAAGUAUAGGAAAUUUCCCGAAUCUGUGGUAUAAUAAAUGGCAAUACCUUGAAAGAGCUUUAUUUUAAAC (((((.((((((.(((..((((((..(((((((((((((.((((....((((((.(((....(((((...((...)).....(((((....)))))..)))))...))).))))))..))))))))))))).....))))....))))))..)))...(((((((((((((((....((....((.......))....))..)))).)))))..))))))........)))))))))))...... (-49.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 812 60 11 151 102 NC_009009:SSA_1494|5end_Conserved_uncharacterized_protein_1500773..1501003_NEGATIVE 288 184 143 181 134 NC_009009:SSA_2084|5end_Phosphotransferase_system_(PTS),_galactitol-specific_IIC_component,_putative_2089424..2089654_NEGATIVE 277 198 151 76 22 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 275 48 8 136 90 NC_009009:SSA_1859|5end_Penicillin-binding_protein-like_factor_A/_recombinase,_putative_1853704..1853934_POSITIVE 273 187 143 77 39 NC_009009:SSA_0408|5end_hypothetical_protein_404684..404914_NEGATIVE 273 55 13 146 94 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 271 185 141 191 148 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 268 183 153 67 37 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 268 206 169 199 158 NC_009009:SSA_1445|5end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447886..1448116_NEGATIVE 267 58 15 144 99 NC_009009:SSA_1072|5end_Glutamate_5-kinase,_putative_1089755..1089985_POSITIVE 265 198 156 211 172 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 264 183 141 43 7 NC_009009:SSA_0415|5end_Permease,_putative_410568..410798_POSITIVE 262 205 162 91 30 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 262 203 161 53 14 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 261 190 142 97 50 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 261 57 17 214 177 NC_009009:SSA_0901|5end_Alpha-acetolactate_decarboxylase,_putative_892447..892677_POSITIVE 260 185 153 208 168 NC_009009:SSA_0543|5end_SecA,_putative_537279..537509_POSITIVE 258 200 172 168 141 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 256 55 12 146 104 NC_009009:SSA_2087|5end_Conserved_uncharacterized_protein_2092657..2092887_NEGATIVE 256 209 168 74 27 NC_009009:SSA_1836|5end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1832236..1832466_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 183 143 141 93 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE 277 198 151 67 13 NC_009009:SSA_1420|3end_Homoserine_O-succinyltransferase,_putative_1429684..1429834_NEGATIVE 273 187 143 64 26 NC_009009:SSA_0409|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_404697..404847_NEGATIVE 271 185 141 91 48 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 261 190 142 75 28 NC_009009:SSA_2071|3end_hypothetical_protein_2074596..2074746_NEGATIVE 261 199 152 118 75 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 261 57 17 64 27 NC_009009:SSA_0900|3end_Tetratricopeptide_repeat_(TPR)_family_protein_892377..892527_POSITIVE 258 200 172 90 63 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 258 199 151 59 2 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 257 193 152 93 49 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 257 199 152 100 48 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 255 141 102 80 38 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 248 157 111 76 31 NC_009009:SSA_2139|3end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2139509..2139659_NEGATIVE 247 198 151 43 4 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 246 189 142 56 1 NC_009009:SSA_0477|3end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_480085..480235_POSITIVE 243 198 151 151 103 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE 240 197 151 60 18 NC_009009:SSA_1540|3end_hypothetical_protein_1544915..1545065_NEGATIVE 238 198 151 107 61 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 238 202 168 115 80 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 238 52 13 141 106 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE