Origin IGS: ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaataatactcaatgaaaatcaaagaccaaactaggaagctagccgcaggttgctcaaaacactgttttgaggctgcagatagagctgacgtggtttgaatttgattttcgaagagtataaatagcttagtgatagaagaaaatagggaaatatggtataatgaaacgatagatttttgaataggaataagatc .........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 gatcttattcctattcaaaaatctatcgtttcattataccatatttccctattttcttctatcactaagctatttatactcttcgaaaatcaaattcaaaccacgtcagctctatctgcagcctcaaaacagtgttttgagcaacctgcggctagcttcctagtttggtctttgattttcattgagtattattctcaggcaccaagcccatttttcaaaaaaataagccgcctgattgggcgactctattttttatagggagattattatgaaaaagttttaggagtttaagttaaggtcttcttaacttatggacttagtatacacttcctagcttaaagtttcc Mask Tandem Repeat Region ================================================ ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaataatactcaatgaaaatcaaagaccaaactaggaagctagccgcaggttgctcaaaacactgttttgaggctgcagatagagctgacgtggtttgaatttgattttcgaagagtataaatagcttagtgatagaagaaaatagggaaatatggtataatgaaacgatagatttttgaataggaataagatc Find is-nt database================================================ Query_seq: SMT_217:SMT_218|SMT_217:SMT_218:hypothetical protein:undecaprenyl pyrophosphate synthetase:->->:149949..150294 346 ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaataatactcaatgaaaatcaaagaccaaactaggaagctagccgcaggttgctcaaaacactgttttgaggctgcagatagagctgacgtggtttgaatttgattttcgaagagtataaatagcttagtgatagaagaaaatagggaaatatggtataatgaaacgatagatttttgaataggaataagatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_217:SMT_218|SMT_217:SMT_218:hypothetical protein:undecaprenyl pyrophosphate synthetase:->->:149949..150294 346 ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaataatactcaatgaaaatcaaagaccaaactaggaagctagccgcaggttgctcaaaacactgttttgaggctgcagatagagctgacgtggtttgaatttgattttcgaagagtataaatagcttagtgatagaagaaaatagggaaatatggtataatgaaacgatagatttttgaataggaataagatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_217:SMT_218|SMT_217:SMT_218:hypothetical protein:undecaprenyl pyrophosphate synthetase:->->:149949..150294 346 ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaataatactcaatgaaaatcaaagaccaaactaggaagctagccgcaggttgctcaaaacactgttttgaggctgcagatagagctgacgtggtttgaatttgattttcgaagagtataaatagcttagtgatagaagaaaatagggaaatatggtataatgaaacgatagatttttgaataggaataagatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 158 Max: 305 Len: 148 Subject: UniRef90_O05164 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 3.0E-6 bit: 53.1 Len: 114 Query Start:158 Query End:271 Subject Strand: null Subject Start: 7 Subject End: 44 ............................................................................................................................................................. I L F E N Q I Q T T S A L S A A S K Q C F E Q P A A S F L V W S L I F I E Y ........................................................................... ............................................................................................................................................................. I L F E N L F K P R Q L P S T T S K Q C F E Q P A A S F L V C S L I F I E Y ........................................................................... Subject: UniRef90_Q04L28 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 3.0E-6 bit: 53.1 Len: 141 Query Start:165 Query End:305 Subject Strand: null Subject Start: 1 Subject End: 43 .................................................................................................................................................................... M K I K D Q T R K L A A G C S K H C F E A A D R A D V V * I * F S K S I N S L V I E E N R E I ......................................... .................................................................................................................................................................... M K I K E Q T R K L A A G C S K H C F E V A D K T D E V - - - - S S K H G F E V V D E T D E V ......................................... Subject: UniRef90_Q04I51 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 5.0E-6 bit: 52.4 Len: 141 Query Start:165 Query End:305 Subject Strand: null Subject Start: 1 Subject End: 43 .................................................................................................................................................................... M K I K D Q T R K L A A G C S K H C F E A A D R A D V V * I * F S K S I N S L V I E E N R E I ......................................... .................................................................................................................................................................... M K I K E Q T R K L A A G C S K H C F E V M D R T D E V - - - - S S K H G F E V V D E T D E V ......................................... ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntggtataatgaaacgatagatttttgaataggaataagatc Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: - Start: 187 End: 345 .......................................................................................................................................................................................... S A L R L N S L V S N Q P Q L Y L Q R P K F K I K S S Y L Y S L S L L F Y P F I T Y H F S L N K F L F L M . Protein_Len: 60 Strand: - Start: 92 End: 340 ........................................................................................... E I F I L S W V L F S A A P Q E F C Q K S A A S L A S T T Q I Q N E F L I F L K T I S S F L S I H Y L S V I S K Q I P M ...... ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntggtataatgaaacgatagatttttgaataggaataagatc 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: 81 Start: 285 End: 314 ............................................................................................................................................................................................................................................................................................ATAGAAGAAAATAGGGAAATATGGTATAAT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntggtataatgaaacgatagatttttgaataggaataagatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -2.9 Tail_Score: -5.41143 Start: 99 End: 123 Full_Region: TCTCCCTATAAAAAA TAGAGTCGCC CAATCA GGCGGCTTA TTTTTTTGAAAAATG ..................................................................................................TAGAGTCGCCCAATCAGGCGGCTTA............................................................................................................................................................................................................................... TransTerm Strand: + Conf: 78 HP_score: -6.2 Tail_Score: -4.79949 Start: 103 End: 120 Full_Region: CCTATAAAAAATAGA GTCGCC CAATCA GGCGGC TTATTTTTTTGAAAA ......................................................................................................GTCGCCCAATCAGGCGGC.................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: SMT_217:SMT_218|SMT_217:SMT_218:hypothetical protein:undecaprenyl pyrophosphate synthetase:->->:149949..150294 346 ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntggtataatgaaacgatagatttttgaataggaataagatc Intra-Species Hit: Count: 1 Min: 1 Max: 346 Len: 346 Subject: smit_SMT_217_SMT_218|hypothetical protein:undecaprenyl pyrophosphate synthetase|POSITIVE:POSITIVE|[149949,150294]|346 HSP 1 e-value: 9.0E-84 bit: 311.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaata............................................................................................................................................................................................. ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaata............................................................................................................................................................................................. HSP 2 e-value: 1.0E-14 bit: 81.8 Len: 41 Query Start:306 Query End:346 Subject Strand: POSITIVE Subject Start: 306 Subject End: 346 .................................................................................................................................................................................................................................................................................................................tggtataatgaaacgatagatttttgaataggaataagatc .................................................................................................................................................................................................................................................................................................................tggtataatgaaacgatagatttttgaataggaataagatc Inter-species Hit: Count: 3 Min: 1 Max: 346 Len: 346 Subject: NC_008533_SPD_0242_SPD_0243|hypothetical protein:undecaprenyl diphosphate synthase|POSITIVE:POSITIVE|[233681,233910]|230 HSP 1 e-value: 2.0E-69 bit: 264.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaata............................................................................................................................................................................................. ggaaactttaagctagggagtgtacactaagttcataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctat-aaaaataaagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaata............................................................................................................................................................................................. HSP 2 e-value: 1.0E-14 bit: 81.8 Len: 41 Query Start:306 Query End:346 Subject Strand: POSITIVE Subject Start: 190 Subject End: 230 .................................................................................................................................................................................................................................................................................................................tggtataatgaaacgatagatttttgaataggaataagatc .................................................................................................................................................................................................................................................................................................................tggtataatgaaacgatagatttttgaataggaataagatc Subject: NC_003098_spr0239_spr0240|hypothetical protein:Undecaprenyl diphosphate synthase|POSITIVE:POSITIVE|[233680,233891]|212 HSP 1 e-value: 2.0E-69 bit: 264.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaata............................................................................................................................................................................................. ggaaactttaagctagggagtgtacactaagttcataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctat-aaaaataaagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaata............................................................................................................................................................................................. Subject: NC_003028_SP_0260_SP_0261|hypothetical protein:undecaprenyl diphosphate synthase|POSITIVE:POSITIVE|[233152,233381]|230 HSP 1 e-value: 2.0E-69 bit: 264.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 ggaaactttaagctaggaagtgtatactaagtccataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctataaaaaatagagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaata............................................................................................................................................................................................. ggaaactttaagctagggagtgtacactaagttcataagttaagaagaccttaacttaaactcctaaaactttttcataataatctccctat-aaaaataaagtcgcccaatcaggcggcttatttttttgaaaaatgggcttggtgcctgagaata............................................................................................................................................................................................. HSP 2 e-value: 1.0E-14 bit: 81.8 Len: 41 Query Start:306 Query End:346 Subject Strand: POSITIVE Subject Start: 190 Subject End: 230 .................................................................................................................................................................................................................................................................................................................tggtataatgaaacgatagatttttgaataggaataagatc .................................................................................................................................................................................................................................................................................................................tggtataatgaaacgatagatttttgaataggaataagatc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAACUUUAAGCUAGGAAGUGUAUACUAAGUCCAUAAGUUAAGAAGACCUUAACUUAAACUCCUAAAACUUUUUCAUAAUAAUCUCCCUAUAAAAAAUAGAGUCGCCCAAUCAGGCGGCUUAUUUUUUUGAAAAAUGGGCUUGGUGCCUGAGAAUAAUACUCAAUGAAAAUCAAAGACCAAACUAGGAAGCUAGCCGCAGGUUGCUCAAAACACUGUUUUGAGGCUGCAGAUAGAGCUGACGUGGUUUGAAUUUGAUUUUCGAAGAGUAUAAAUAGCUUAGUGAUAGAAGAAAAUAGGGAAAUAUGGUAUAAUGAAACGAUAGAUUUUUGAAUAGGAAUAAGAUC (....).((((((((.........((((((((((.(((((((((.....)))))))))............(((((((...............(((((((.((((((((......)))))))))))))))))))))).))))))))))..........((((((..(((((((((((...((((((((..((((..(.((((....((((((((...)))))))).)))).)....))))..).)))))))..)))))))))))..))))))...)))))))).............((((((..(((.((........)).)))..))))))............... (-94.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCUUAUUCCUAUUCAAAAAUCUAUCGUUUCAUUAUACCAUAUUUCCCUAUUUUCUUCUAUCACUAAGCUAUUUAUACUCUUCGAAAAUCAAAUUCAAACCACGUCAGCUCUAUCUGCAGCCUCAAAACAGUGUUUUGAGCAACCUGCGGCUAGCUUCCUAGUUUGGUCUUUGAUUUUCAUUGAGUAUUAUUCUCAGGCACCAAGCCCAUUUUUCAAAAAAAUAAGCCGCCUGAUUGGGCGACUCUAUUUUUUAUAGGGAGAUUAUUAUGAAAAAGUUUUAGGAGUUUAAGUUAAGGUCUUCUUAACUUAUGGACUUAGUAUACACUUCCUAGCUUAAAGUUUCC ......(((((((...........((..((((((.(((....(((((((((........................((((((...((((((((((.((((((...(..((((....((((((.((((((((...))))))))....))))))..))))..)..))))))..))))))))))...))))))........(((.....))).........((((((((((.(((((....))))).)).)))))))).)))))))))))).))))))..))..))))))).(((((((((.....))))))))).(((...(((....))))))............... (-83.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 846 210 161 224 175 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 822 240 191 230 180 smit:SMT_150|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_98787..99017_POSITIVE 815 230 181 184 135 smit:SMT_163|5end_cardiolipin_synthetase_107309..107539_POSITIVE 788 220 171 167 118 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 787 210 161 167 118 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 739 207 161 203 155 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 739 207 161 155 107 smit:SMT_483|5end_transcriptional_activator_TipA,_putative_418827..419057_POSITIVE 734 208 161 182 133 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 730 240 191 206 157 smit:SMT_1544|5end_mevalonate_kinase_1528884..1529114_NEGATIVE 708 207 161 169 121 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 708 207 161 217 169 smit:SMT_1138|5end_hypothetical_protein_1079547..1079777_NEGATIVE 708 207 161 194 146 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 708 207 161 178 130 smit:SMT_130|5end_capsular_polysaccharide_biosynthesis_protein_80995..81225_POSITIVE 687 207 161 168 120 smit:SMT_1963|5end_ribonuclease_BN,_putative_1896462..1896692_NEGATIVE 683 207 161 220 172 smit:SMT_1179|5end_aldose_1-epimerase_1137854..1138084_NEGATIVE 665 270 221 64 15 smit:SMT_149|5end_hypothetical_protein_predicted_by_Glimmer/Critica_98592..98822_POSITIVE 664 239 191 190 142 smit:SMT_775|5end_alpha-acetolactate_decarboxylase_685972..686202_NEGATIVE 662 207 161 166 118 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 612 202 161 230 189 smit:SMT_443|5end_hydroxyethylthiazole_kinase_382555..382785_POSITIVE 599 270 221 52 1 smit:SMT_2109|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999099..1999329_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 822 240 191 148 98 smit:SMT_149|3end_hypothetical_protein_predicted_by_Glimmer/Critica_98785..98935_POSITIVE 669 248 202 47 1 smit:SMT_455|3end_cation_transport_ATPase_393993..394143_POSITIVE 651 270 221 90 42 smit:SMT_1489|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1470714..1470864_POSITIVE 607 270 221 83 41 smit:SMT_1766|3end_sucrose-6-phosphate_hydrolase_1743101..1743251_POSITIVE 601 270 221 55 7 smit:SMT_1626|3end_undecaprenyl-diphosphatase_1615183..1615333_NEGATIVE 599 270 221 90 39 smit:SMT_2109|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999061..1999211_NEGATIVE 599 270 221 90 39 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 599 270 221 90 39 smit:SMT_1180|3end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1138036..1138186_NEGATIVE 597 270 221 62 13 smit:SMT_1144|3end_K02026_multiple_sugar_transport_system_permease_protein_1089144..1089294_POSITIVE 594 270 221 90 39 smit:SMT_890|3end_K02029_polar_amino_acid_transport_system_permease_protein_837692..837842_POSITIVE 584 270 221 86 44 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE 584 270 221 67 25 smit:SMT_1671|3end_hypothetical_protein_1659392..1659542_NEGATIVE 577 270 224 90 46 smit:SMT_913|3end_putative_sucrose-specific_PTS_permease,_enzyme_II_863923..864073_NEGATIVE 573 270 224 46 1 smit:SMT_452|3end_phosphomethylpyrimidine_kinase_389777..389927_NEGATIVE 569 270 221 90 39 smit:SMT_1140|3end_glycogen_phosphorylase_1081316..1081466_NEGATIVE 567 268 221 52 3 smit:SMT_442|3end_transcriptional_regulator,_putative_382400..382550_POSITIVE 553 280 231 57 3 smit:SMT_1076|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_/_dihydroneopterin_aldolase_1014001..1014151_NEGATIVE 546 207 171 39 1 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 544 207 171 39 1 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 532 270 221 55 6 smit:SMT_1380|3end_pyrroline-5-carboxylate_reductase_1357667..1357817_NEGATIVE