Origin IGS: cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag .........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 ctgagcaacagcccctgtaaaaaagaatgctaaagcaataacagtagttaccgtccttagtttagttgaaaaataggtaatcatattcattatagattttaatgttgtctgttagtgttgaacttgctgcaaagtaagtgtatatttgtaaaaggcaatataaaatttgttgcacagagtggtaaaattgtcttaatgcaacaaatgtgtgtgaagttgaaagattattgcttgtattgtactgtaaaaagcgcgaagcagcaatcttgaaaggttgaaaataaaggctgacgatgataaaaatatgttgtattttctttacttataattcttattaatacacaaaaacttgtatctttgcagatatatcatcttgagaaagagtagtgtagaaaaaaggaaacaactaaaacgacagggaaaag Mask Tandem Repeat Region ================================================ cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag Find is-nt database================================================ Query_seq: PI1763:PI1764|PI1763:PI1764:two-component system sensor histidine kinase/response regulator:conserved hypothetical protein:->->:1688663..1689087 425 cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1763:PI1764|PI1763:PI1764:two-component system sensor histidine kinase/response regulator:conserved hypothetical protein:->->:1688663..1689087 425 cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1763:PI1764|PI1763:PI1764:two-component system sensor histidine kinase/response regulator:conserved hypothetical protein:->->:1688663..1689087 425 cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 61 End: 198 ............................................................ M C K D T S F C V L I R I I S K E N T T Y F Y H R Q P L F S T F Q D C C F A L F T V Q Y K Q ................................................................................................................................................................................................................................... Protein_Len: 37 Strand: + Start: 120 End: 230 ....................................................................................................................... M F L S S S A F I F N L S R L L L R A F Y S T I Q A I I F Q L H T H L L H ................................................................................................................................................................................................... Protein_Len: 35 Strand: + Start: 220 End: 324 ........................................................................................................................................................................................................................... M C C I K T I L P L C A T N F I L P F T N I H L L C S K F N T N R Q H ..................................................................................................... Protein_Len: 60 Strand: + Start: 113 End: 361 ................................................................................................................ M Q H I F I I V S L Y F Q P F K I A A S R F L Q Y N T S N N L S T S H T F V A L R Q F Y H S V Q Q I L Y C L L Q I Y T Y ................................................................ Protein_Len: 31 Strand: + Start: 333 End: 425 ............................................................................................................................................................................................................................................................................................................................................ M M N M I T Y F S T K L R T V T T V I A L A F F F T G A V A Q Protein_Len: 53 Strand: - Start: 159 End: 317 .............................................................................................................................................................. S Q Q K A S K V T C Y L C Y D K L K V C M Q Q M L V I K G S Q A V F K I N G K V F I C K S Q L L N L V L M ............................................................................................................ cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag 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: 161 End: 190 ................................................................................................................................................................ATTGCTGCTTCGCGCTTTTTACAGTACAAT........................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 280 End: 309 .......................................................................................................................................................................................................................................................................................GTTGAACTTGCTGCAAAGTAAGTGTATATT.................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 240 End: 269 ...............................................................................................................................................................................................................................................TTTACCACTCTGTGCAACAAATTTTATATT............................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1763:PI1764|PI1763:PI1764:two-component system sensor histidine kinase/response regulator:conserved hypothetical protein:->->:1688663..1689087 425 cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag Intra-Species Hit: Count: 1 Min: 1 Max: 425 Len: 425 Subject: pint_PI1763_PI1764|two-component system sensor histidine kinase/response regulator:conserved hypothetical protein|POSITIVE:POSITIVE|[1688663,1689087]|425 HSP 1 e-value: 0.0 bit: 842.0 Len: 425 Query Start:1 Query End:425 Subject Strand: POSITIVE Subject Start: 1 Subject End: 425 cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag cttttccctgtcgttttagttgtttccttttttctacactactctttctcaagatgatatatctgcaaagatacaagtttttgtgtattaataagaattataagtaaagaaaatacaacatatttttatcatcgtcagcctttattttcaacctttcaagattgctgcttcgcgctttttacagtacaatacaagcaataatctttcaacttcacacacatttgttgcattaagacaattttaccactctgtgcaacaaattttatattgccttttacaaatatacacttactttgcagcaagttcaacactaacagacaacattaaaatctataatgaatatgattacctatttttcaactaaactaaggacggtaactactgttattgctttagcattcttttttacaggggctgttgctcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCCCUGUCGUUUUAGUUGUUUCCUUUUUUCUACACUACUCUUUCUCAAGAUGAUAUAUCUGCAAAGAUACAAGUUUUUGUGUAUUAAUAAGAAUUAUAAGUAAAGAAAAUACAACAUAUUUUUAUCAUCGUCAGCCUUUAUUUUCAACCUUUCAAGAUUGCUGCUUCGCGCUUUUUACAGUACAAUACAAGCAAUAAUCUUUCAACUUCACACACAUUUGUUGCAUUAAGACAAUUUUACCACUCUGUGCAACAAAUUUUAUAUUGCCUUUUACAAAUAUACACUUACUUUGCAGCAAGUUCAACACUAACAGACAACAUUAAAAUCUAUAAUGAAUAUGAUUACCUAUUUUUCAACUAAACUAAGGACGGUAACUACUGUUAUUGCUUUAGCAUUCUUUUUUACAGGGGCUGUUGCUCAG ....(((((((...((((((((..............................(.(((.....((((((((.....(((((((((......)))))))))....((((((..((((..........................................(((((((.(((((.(..((......))..).....))))).)))))))..............(((((((((((..((............))..)))))))))))....))))...)))))).............)))))))).....))).)............(((((.......)))))...................))))))))((((((.(((((((....)))))))))))))...........)))))))........... (-71.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAGCAACAGCCCCUGUAAAAAAGAAUGCUAAAGCAAUAACAGUAGUUACCGUCCUUAGUUUAGUUGAAAAAUAGGUAAUCAUAUUCAUUAUAGAUUUUAAUGUUGUCUGUUAGUGUUGAACUUGCUGCAAAGUAAGUGUAUAUUUGUAAAAGGCAAUAUAAAAUUUGUUGCACAGAGUGGUAAAAUUGUCUUAAUGCAACAAAUGUGUGUGAAGUUGAAAGAUUAUUGCUUGUAUUGUACUGUAAAAAGCGCGAAGCAGCAAUCUUGAAAGGUUGAAAAUAAAGGCUGACGAUGAUAAAAAUAUGUUGUAUUUUCUUUACUUAUAAUUCUUAUUAAUACACAAAAACUUGUAUCUUUGCAGAUAUAUCAUCUUGAGAAAGAGUAGUGUAGAAAAAAGGAAACAACUAAAACGACAGGGAAAAG ............((((((...((((((.((....)).((((((....(((.((((.(((((((.................((((((.((((..((((((((.((((((((...(((((...(((((((....)))))))..)))))......))))))))))))))))((((((..(((............)))..)))))).)))).))))))..((..((((((.(((((....(((..((......))..)))))))).))))))..))............))))))).)))).))).....))))))...))))))........(((((.((..(((((.......(((((((....)))))))...((((....))))...)))))..)).))))).............))))))..... (-94.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 173 133 131 89 pint:PI0252|5end_conserved_hypothetical_protein_247761..247991_POSITIVE 307 177 133 208 156 pint:PI1000|5end_conserved_hypothetical_protein_923332..923562_POSITIVE 295 320 271 111 48 pint:PI1067|5end_thymidylate_synthase_983940..984170_POSITIVE 290 175 134 88 44 pint:PI1705|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1621781..1622011_POSITIVE 288 179 131 115 65 pint:PI0027|5end_aminopeptidase_C_30468..30698_POSITIVE 283 419 382 167 124 pint:PI0428|5end_hypothetical_protein_393080..393310_POSITIVE 279 420 373 86 40 pint:PI1946|5end_hypothetical_protein_1902713..1902943_POSITIVE 279 418 371 61 27 pint:PI1933|5end_hypothetical_protein_1879925..1880155_POSITIVE 279 416 379 198 158 pint:PI0764|5end_permease_697962..698192_POSITIVE 278 420 373 123 62 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 277 206 163 58 13 pint:PI1949|5end_aminotransferase,_class_V_1903218..1903448_POSITIVE 270 418 373 146 96 pint:PI0164|5end_conserved_hypothetical_protein_158478..158708_POSITIVE 265 178 132 170 115 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 264 195 153 54 15 pint:PI0810|5end_hypothetical_protein_746743..746973_POSITIVE 264 195 153 49 10 pint:PI0811|5end_protease/hemagglutinin_PrtT,_streptopain_family_746738..746968_POSITIVE 263 179 131 121 77 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 260 420 375 62 8 pint:PI2096|5end_conserved_hypothetical_protein;_possible_phosphoesterase_2050268..2050498_POSITIVE 260 184 147 216 181 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 260 184 147 49 14 pint:PI0196|5end_hypothetical_protein_188435..188665_POSITIVE 259 179 133 64 6 pint:PI0804|5end_conserved_hypothetical_protein;_possible_membrane_protein_741934..742164_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 173 133 100 58 pint:PI0251|3end_hypothetical_protein_247810..247960_POSITIVE 307 177 133 132 80 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 288 179 131 104 54 pint:PI0026|3end_two-component_system_response_regulator_30537..30687_POSITIVE 284 210 163 97 53 pint:PI0147|3end_HIT_family_protein_141308..141458_POSITIVE 283 419 382 95 52 pint:PI0427|3end_conserved_hypothetical_protein_393088..393238_POSITIVE 270 418 379 127 88 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 266 180 132 113 76 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 265 181 150 73 35 pint:PI0642|3end_thioredoxin_family_protein_585582..585732_POSITIVE 265 178 132 150 95 pint:PI0284|3end_flavoprotein_A_270157..270307_POSITIVE 263 179 131 63 19 pint:PI1549|3end_conserved_hypothetical_protein_1467382..1467532_POSITIVE 257 179 133 144 104 pint:PI1686|3end_hypothetical_protein_1601898..1602048_POSITIVE 256 176 138 123 76 pint:PI0366|3end_conserved_hypothetical_protein_337894..338044_POSITIVE 253 180 134 146 103 pint:PI1215|3end_orotidine_5'-phosphate_decarboxylase_1134871..1135021_POSITIVE 252 418 373 144 96 pint:PI1482|3end_hypothetical_protein_1404645..1404795_POSITIVE 251 275 233 150 100 pint:PI1660|3end_hypothetical_protein_1575005..1575155_POSITIVE 249 195 162 133 91 pint:PI1324|3end_conserved_hypothetical_protein_1243025..1243175_POSITIVE 249 176 132 127 84 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE 246 177 135 140 92 pint:PI0487|3end_50S_ribosomal_protein_L17_446703..446853_POSITIVE 244 180 136 54 4 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 244 196 153 138 94 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE