Origin IGS: gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttctccttcctctgctaacttttacagtcagcagttttctcatgccctctgaaaatcaaaaagtaatgaaaacctcccatcagaagctccattcttattttgatcctctttaagcatcagaatatatatgtatcttaatcctaacatgttttgcctcgttttgcaagcattttttgctccttttatttacccccaaacaaatttaaacacttgttcaaatattgtctatttttattcttctttgccctatcttcctttaaatggacaatgagaatacaagaaaaagaccagcttttgctagtctttccttattacagttttgtacttgttctctacaagatcaaagattccaaactaactgc Mask Tandem Repeat Region ================================================ gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa Find is-nt database================================================ Query_seq: SSA_0302:SSA_0303|SSA_0302:SSA_0303:Phosphoglycerate kinase, putative:surface protein C:->->:296227..296590 364 gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0302:SSA_0303|SSA_0302:SSA_0303:Phosphoglycerate kinase, putative:surface protein C:->->:296227..296590 364 gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0302:SSA_0303|SSA_0302:SSA_0303:Phosphoglycerate kinase, putative:surface protein C:->->:296227..296590 364 gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 88 End: 177 ....................................................................................... M L I V H L K E D R A K K N K N R Q Y L N K C L N L F G G K ........................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 161 End: 250 ................................................................................................................................................................ M C L G V N K R S K K C L Q N E A K H V R I K I H I Y S D A .................................................................................................................. Protein_Len: 48 Strand: + Start: 177 End: 320 ................................................................................................................................................................................ M K G A K N A C K T R Q N M L G L R Y I Y I L M L K E D Q N K N G A S D G R F S L L F D F Q R A ............................................ Protein_Len: 33 Strand: - Start: 253 End: 351 ............................................................................................................................................................................................................................................................ L P D F Y S H L K Q H S T K M V K Q N E S P M L F S S V T F T L M ............. Protein_Len: 51 Strand: - Start: 95 End: 247 .............................................................................................. Q G N L P L Y P L S S Y F Y V I N S C T N L N T Q P Y I F P A F F A Q L V L C F M N P N L Y M Y I R M ..................................................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 212 .. V L V F S Y Y P F V L L L Q D K E Q I R M T W K F S S L A F F F L F L C Y K F L H K F K N P P L Y F S C F I S A F R P M ........................................................................................................................................................ Protein_Len: 34 Strand: - Start: 1 End: 102 C N T Q F R Q D Q L S C T C F Q L L S L S A F A P R K R T N E N D M ...................................................................................................................................................................................................................................................................... gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa 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: 196 End: 225 ...................................................................................................................................................................................................CTTGCAAAACGAGGCAAAACATGTTAGGAT........................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -7.7 Tail_Score: -5.31072 Start: 60 End: 77 Full_Region: ACTGTAATAAGGAAA GACTAGC AAAA GCTGGTC TTTTTCTTGTATTCT ...........................................................GACTAGCAAAAGCTGGTC............................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 47 HP_score: -4.0 Tail_Score: -3.11297 Start: 239 End: 267 Full_Region: cagaagctccattct tattttgatcct cttta agcatcagaata tatatgtatcttaat ..............................................................................................................................................................................................................................................tattttgatcctctttaagcatcagaata................................................................................................. Find igs database================================================ Query_seq: SSA_0302:SSA_0303|SSA_0302:SSA_0303:Phosphoglycerate kinase, putative:surface protein C:->->:296227..296590 364 gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 364 Len: 364 Subject: NC_009009_SSA_0302_SSA_0303|Phosphoglycerate kinase, putative:surface protein C|POSITIVE:POSITIVE|[296227,296590]|364 HSP 1 e-value: 0.0 bit: 722.0 Len: 364 Query Start:1 Query End:364 Subject Strand: POSITIVE Subject Start: 1 Subject End: 364 gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa gcagttagtttggaatctttgatcttgtagagaacaagtacaaaactgtaataaggaaagactagcaaaagctggtctttttcttgtattctcattgtccatttaaaggaagatagggcaaagaagaataaaaatagacaatatttgaacaagtgtttaaatttgtttgggggtaaataaaaggagcaaaaaatgcttgcaaaacgaggcaaaacatgttaggattaagatacatatatattctgatgcttaaagaggatcaaaataagaatggagcttctgatgggaggttttcattactttttgattttcagagggcatgagaaaactgctgactgtaaaagttagcagaggaaggagaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGUUAGUUUGGAAUCUUUGAUCUUGUAGAGAACAAGUACAAAACUGUAAUAAGGAAAGACUAGCAAAAGCUGGUCUUUUUCUUGUAUUCUCAUUGUCCAUUUAAAGGAAGAUAGGGCAAAGAAGAAUAAAAAUAGACAAUAUUUGAACAAGUGUUUAAAUUUGUUUGGGGGUAAAUAAAAGGAGCAAAAAAUGCUUGCAAAACGAGGCAAAACAUGUUAGGAUUAAGAUACAUAUAUAUUCUGAUGCUUAAAGAGGAUCAAAAUAAGAAUGGAGCUUCUGAUGGGAGGUUUUCAUUACUUUUUGAUUUUCAGAGGGCAUGAGAAAACUGCUGACUGUAAAAGUUAGCAGAGGAAGGAGAAAA ((((((..((((...((((((......)))))).)))).....)))))).((((((((((((((((....))))))).))))))))).(((((((.((((...............(((((....((((((....(((((((.((((((((....)))))))))))))))...(((........(((((.....)))))....((((.(......).))))..........))).....))))))..)))))...(((((((((((....((((((((((((....))))).)))))))...)))))))))))...)))))))))))..(((((((((.....)))))))))............. (-100.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUCCUUCCUCUGCUAACUUUUACAGUCAGCAGUUUUCUCAUGCCCUCUGAAAAUCAAAAAGUAAUGAAAACCUCCCAUCAGAAGCUCCAUUCUUAUUUUGAUCCUCUUUAAGCAUCAGAAUAUAUAUGUAUCUUAAUCCUAACAUGUUUUGCCUCGUUUUGCAAGCAUUUUUUGCUCCUUUUAUUUACCCCCAAACAAAUUUAAACACUUGUUCAAAUAUUGUCUAUUUUUAUUCUUCUUUGCCCUAUCUUCCUUUAAAUGGACAAUGAGAAUACAAGAAAAAGACCAGCUUUUGCUAGUCUUUCCUUAUUACAGUUUUGUACUUGUUCUCUACAAGAUCAAAGAUUCCAAACUAACUGC .............(((((.(((.....))).)))))............((.(((....(((((.(((((((............((.(((..(((...(((((((((.((.....)).)))))))))...)))...............((((((.((........)))))))).....))).))............................(((((.....((((((((((((...........................)))))))))))).....)))))..((((((.(((....))).))))))..)))))))..)))))..(((((.....))))).))).))................ (-59.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 108 61 164 116 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 312 358 312 62 25 NC_009009:SSA_2204|5end_hypothetical_protein_2204663..2204893_POSITIVE 301 360 314 155 111 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 293 360 317 215 170 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 288 353 317 50 20 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 283 234 196 55 16 NC_009009:SSA_2149|5end_hypothetical_protein_2150821..2151051_NEGATIVE 274 320 271 230 178 NC_009009:SSA_1954|5end_Aminotransferase,_class-V,_putative_1951298..1951528_NEGATIVE 274 355 311 212 162 NC_009009:SSA_1133|5end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159397..1159627_POSITIVE 274 358 314 68 30 NC_009009:SSA_0260|5end_Manganese/Zinc_ABC_transporter_substrate-binding_lipoprotein_precursor,_putative_254585..254815_NEGATIVE 273 346 313 107 76 NC_009009:SSA_0327|5end_Glycosyltransferase,_putative_319979..320209_POSITIVE 273 320 278 66 23 NC_009009:SSA_0091|5end_V-type_sodium_ATPase,_subunit_A,_putative_91037..91267_POSITIVE 272 119 71 187 138 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 272 352 311 203 164 NC_009009:SSA_0944|5end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_951741..951971_POSITIVE 270 99 57 152 112 NC_009009:SSA_2137|5end_hypothetical_protein_2138412..2138642_NEGATIVE 268 100 62 96 52 NC_009009:SSA_1902|5end_tRNA_(guanine-N(7)-)-methyltransferase,_putative_1897391..1897621_NEGATIVE 268 360 312 223 161 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 266 349 305 70 18 NC_009009:SSA_0777|5end_Glycogen_biosynthesis_protein_GlgD,_putative_759430..759660_POSITIVE 264 94 53 178 137 NC_009009:SSA_0154|5end_hypothetical_protein_149836..150066_POSITIVE 263 310 261 88 28 NC_009009:SSA_1682|5end_hypothetical_protein_1676885..1677115_NEGATIVE 260 335 293 206 156 NC_009009:SSA_2298|5end_Serine_protease_containing_a_PDZ_domain,_putative_2300603..2300833_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 108 61 138 90 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 314 87 51 40 4 NC_009009:SSA_0302|3end_Phosphoglycerate_kinase,_putative_296166..296316_POSITIVE 301 360 314 150 106 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 285 87 46 98 54 NC_009009:SSA_0626|3end_hypothetical_protein_617212..617362_POSITIVE 274 358 314 48 10 NC_009009:SSA_0261|3end_ABC-type_Mn2+/Zn2+_transport_systems,_permease_component,_putative_254605..254755_NEGATIVE 270 99 57 102 62 NC_009009:SSA_2138|3end_RNA-binding_protein,_Jag_family,_putative_2138462..2138612_NEGATIVE 268 100 62 99 55 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 266 349 305 80 28 NC_009009:SSA_0776|3end_Glucose-1-phosphate_adenylyltransferase,_putative_759520..759670_POSITIVE 256 360 318 83 34 NC_009009:SSA_0615|3end_RggD,_putative_608326..608476_NEGATIVE 254 360 323 144 99 NC_009009:SSA_0735|3end_Integral_membrane_protein,_putative_717680..717830_POSITIVE 253 335 292 85 30 NC_009009:SSA_0441|3end_hypothetical_protein_442175..442325_POSITIVE 252 354 319 53 19 NC_009009:SSA_2388|3end_hypothetical_protein_2031667..2031817_NEGATIVE 251 360 312 62 4 NC_009009:SSA_0425|3end_Glycosyltransferase,_putative_422230..422380_NEGATIVE 248 119 71 63 20 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 247 349 301 52 5 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 247 118 72 74 29 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 246 338 299 146 100 NC_009009:SSA_1229|3end_hypothetical_protein_1252314..1252464_NEGATIVE 245 119 71 126 75 NC_009009:SSA_2158|3end_Methyltransferase,_putative_2158421..2158571_NEGATIVE 244 319 274 143 99 NC_009009:SSA_1686|3end_hypothetical_protein_1680470..1680620_POSITIVE 244 109 62 121 86 NC_009009:SSA_0798|3end_ABC_transporter_membrane-spanning_permease-macrolide_efflux,_putative_781724..781874_POSITIVE