Origin IGS: gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc .........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 gatttttcaaatagcgatgtgaaatgataaatctggatattaacgtctaggaataggataaatttaaccaatattaataaatcaaactaagaattaagagttaacgaaatcagaaaaaaactgaaatattcgtttgctctttttgtatgtttaaatctttaagaaagattttttctgtttgggataataaaaaactattccgtcttaaaattttaaagaaagtcggaaatcatttttattataataaattctacttcaatactttttaaaaactctccaatttttataaaaaacattccaaaacattgtttttatctgtattcgattgacaaattttttattggttataaaatcgtattataagataattataataagtagattgctctcagataaaatgaaagcggttaccaaaaggaggattac Mask Tandem Repeat Region ================================================ gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc Find is-nt database================================================ Query_seq: SMT_1253:SMT_1254|SMT_1253:SMT_1254:beta-galactosidase:hypothetical protein predicted by Glimmer/Critica:<-<-:1220238..1220663 426 gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1253:SMT_1254|SMT_1253:SMT_1254:beta-galactosidase:hypothetical protein predicted by Glimmer/Critica:<-<-:1220238..1220663 426 gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1253:SMT_1254|SMT_1253:SMT_1254:beta-galactosidase:hypothetical protein predicted by Glimmer/Critica:<-<-:1220238..1220663 426 gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 79 End: 168 .............................................................................. M T N K K F V N R I Q I K T M F W N V F Y K N W R V F K K Y .................................................................................................................................................................................................................................................................. Protein_Len: 33 Strand: + Start: 216 End: 314 ....................................................................................................................................................................................................................... M L R R N S F L L S Q T E K I F L K D L N I Q K E Q T N I S V F F ................................................................................................................ Protein_Len: 47 Strand: - Start: 161 End: 301 ................................................................................................................................................................ F T N F Y F K N Y Y F H N G V K K L I K L R F L K K N D W V S F I K R L S K F M C F S C V F M ............................................................................................................................. Protein_Len: 44 Strand: - Start: 67 End: 198 .................................................................. L V I K Y G I F F K D I S Y L Y F C H K P I N K I F I P S N K F L I S T S N I I I F I M .................................................................................................................................................................................................................................... Protein_Len: 40 Strand: - Start: 3 End: 122 .. I R R K T V A K M K D S L L R S I I I I K Y Y S K I V L L F N T L R I C I F V M ................................................................................................................................................................................................................................................................................................................ gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc 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: 30 End: 59 .............................TTTATCTGAGAGCAATCTACTTATTATAAT............................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 157 End: 186 ............................................................................................................................................................TTTAAAAAGTATTGAAGTAGAATTTATTAT................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -3.0 Tail_Score: -3.2241 Start: 49 End: 73 Full_Region: TCTGAGAGCAATCTA CTTATTATAA TTATC TTATAATACG ATTTTATAACCAATA ................................................CTTATTATAATTATCTTATAATACG................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 39 HP_score: -3.0 Tail_Score: -2.58714 Start: 49 End: 73 Full_Region: tattggttataaaat cgtattataa gataa ttataataag tagattgctctcaga ................................................cgtattataagataattataataag................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 79 HP_score: -4.9 Tail_Score: -5.56264 Start: 259 End: 271 Full_Region: ttttgtatgtttaaa tcttt aag aaaga ttttttctgtttggg ..................................................................................................................................................................................................................................................................tctttaagaaaga........................................................................................................................................................... Find igs database================================================ Query_seq: SMT_1253:SMT_1254|SMT_1253:SMT_1254:beta-galactosidase:hypothetical protein predicted by Glimmer/Critica:<-<-:1220238..1220663 426 gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 426 Len: 426 Subject: smit_SMT_1253_SMT_1254|beta-galactosidase:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:NEGATIVE|[1220238,1220663]|426 HSP 1 e-value: 0.0 bit: 803.0 Len: 426 Query Start:1 Query End:426 Subject Strand: POSITIVE Subject Start: 1 Subject End: 426 gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagnnnnnnnctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc gtaatcctccttttggtaaccgctttcattttatctgagagcaatctacttattataattatcttataatacgattttataaccaataaaaaatttgtcaatcgaatacagataaaaacaatgttttggaatgttttttataaaaattggagagtttttaaaaagtattgaagtagaatttattataataaaaatgatttccgactttctttaaaattttaagacggaatagttttttattatcccaaacagaaaaaatctttcttaaagatttaaacatacaaaaagagcaaacgaatatttcagtttttttctgatttcgttaactcttaattcttagtttgatttattaatattggttaaatttatcctattcctagacgttaatatccagatttatcatttcacatcgctatttgaaaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAUCCUCCUUUUGGUAACCGCUUUCAUUUUAUCUGAGAGCAAUCUACUUAUUAUAAUUAUCUUAUAAUACGAUUUUAUAACCAAUAAAAAAUUUGUCAAUCGAAUACAGAUAAAAACAAUGUUUUGGAAUGUUUUUUAUAAAAAUUGGAGAGUUUUUAAAAAGUAUUGAAGUAGAAUUUAUUAUAAUAAAAAUGAUUUCCGACUUUCUUUAAAAUUUUAAGACGGAAUAGUUUUUUAUUAUCCCAAACAGAAAAAAUCUUUCUUAAAGAUUUAAACAUACAAAAAGAGCAAACGAAUAUUUCAGUUUUUUUCUGAUUUCGUUAACUCUUAAUUCUUAGUUUGAUUUAUUAAUAUUGGUUAAAUUUAUCCUAUUCCUAGACGUUAAUAUCCAGAUUUAUCAUUUCACAUCGCUAUUUGAAAAAUC ............(((((....(((((((.......)))))))......(.((((((((.....)))))))).)........)))))...............(((((((..(((......(((((((.((((((...............(((.....(((((..((((((((.............((((((((((....(((((.(((.............))).)))))....))))))))))..(((((((((.(((((((.....)))))))...........(((((..((((((....((((.......)))).))))))..)))))..))))..))))).....))))))))..)))))....))))))))).)))))))........((....)).......)))..)))))))...... (-76.78) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUUCAAAUAGCGAUGUGAAAUGAUAAAUCUGGAUAUUAACGUCUAGGAAUAGGAUAAAUUUAACCAAUAUUAAUAAAUCAAACUAAGAAUUAAGAGUUAACGAAAUCAGAAAAAAACUGAAAUAUUCGUUUGCUCUUUUUGUAUGUUUAAAUCUUUAAGAAAGAUUUUUUCUGUUUGGGAUAAUAAAAAACUAUUCCGUCUUAAAAUUUUAAAGAAAGUCGGAAAUCAUUUUUAUUAUAAUAAAUUCUACUUCAAUACUUUUUAAAAACUCUCCAAUUUUUAUAAAAAACAUUCCAAAACAUUGUUUUUAUCUGUAUUCGAUUGACAAAUUUUUUAUUGGUUAUAAAAUCGUAUUAUAAGAUAAUUAUAAUAAGUAGAUUGCUCUCAGAUAAAAUGAAAGCGGUUACCAAAAGGAGGAUUAC ((((((((.....(((((.............(((((((......))))))).............(((((((((..((....((((..((((((((((((((.((((((.((((.......))))....)))))).))))))...((((....(((((((.....))))))).....(((((..((((((((((....(((((.(((.............))).)))))....))))))))))..))))).........))))................))))))))..(((((((...........)))))))............)))).....))..)))))))))....)))))(((((((.....))))))).....(((((((.(((.......))).))))))).......)))))))).. (-76.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 853 50 1 141 92 smit:SMT_1253|5end_beta-galactosidase_1220147..1220377_NEGATIVE 253 46 1 187 137 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 244 48 8 221 190 smit:SMT_1248|5end_Na+/H+_antiporter_1210529..1210759_NEGATIVE 240 42 6 209 174 smit:SMT_109|5end_beta-galactosidase_53925..54155_POSITIVE 236 60 11 115 63 smit:SMT_543|5end_topoisomerase_IV_subunit_B_458372..458602_POSITIVE 236 50 4 109 60 smit:SMT_414|5end_K03665_GTP-binding_protein_HflX_357554..357784_POSITIVE 230 47 5 222 186 smit:SMT_967|5end_K01992_ABC-2_type_transport_system_permease_protein_913297..913527_NEGATIVE 230 236 194 165 121 smit:SMT_180|5end_50S_ribosomal_protein_L14_119678..119908_POSITIVE 229 48 9 214 173 smit:SMT_1543|5end_diphosphomevalonate_decarboxylase_1528024..1528254_NEGATIVE 228 48 7 56 28 smit:SMT_1736|5end_acetyltransferase,_GNAT_family_1719522..1719752_POSITIVE 226 420 371 88 42 smit:SMT_1668|5end_K+_transport_system,_NAD-binding_component_1658288..1658518_NEGATIVE 226 344 301 127 91 smit:SMT_748|5end_prephenate_dehydratase_653498..653728_NEGATIVE 226 47 10 46 5 smit:SMT_675|5end_DNA_repair_protein_582977..583207_NEGATIVE 223 403 370 101 70 smit:SMT_1789|5end_hypothetical_protein_1765318..1765548_POSITIVE 223 414 376 180 146 smit:SMT_1426|5end_K03095_SprT-like_protein_1411313..1411543_NEGATIVE 223 48 18 175 144 smit:SMT_1396|5end_uracil-DNA_glycosylase_1372064..1372294_POSITIVE 221 43 4 146 95 smit:SMT_1028|5end_ABC-type_sugar_transport_system,_permease_component_964363..964593_NEGATIVE 220 42 5 146 100 smit:SMT_875|5end_nitroreductase_family_protein_823384..823614_NEGATIVE 220 35 5 129 99 smit:SMT_258|5end_alpha-glucosidase,_family_31_of_glycosyl_hydrolase_195049..195279_POSITIVE 219 181 142 179 143 smit:SMT_1811|5end_hypothetical_protein_1785654..1785884_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 42 6 77 42 smit:SMT_108|3end_hypothetical_protein_53873..54023_POSITIVE 236 60 11 63 11 smit:SMT_542|3end_hypothetical_protein_458400..458550_POSITIVE 236 50 4 116 67 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 230 236 194 139 95 smit:SMT_179|3end_ribosomal_protein_S17_119732..119882_POSITIVE 226 420 371 74 28 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 226 344 301 130 94 smit:SMT_749|3end_shikimate_kinase_653495..653645_NEGATIVE 223 48 18 113 82 smit:SMT_1395|3end_K07025_putative_hydrolase_of_the_HAD_superfamily_1372082..1372232_POSITIVE 223 49 4 120 83 smit:SMT_409|3end_pneumococcal_surface_protein,_putative_354406..354556_POSITIVE 221 43 4 127 76 smit:SMT_1029|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_964382..964532_NEGATIVE 220 35 5 132 102 smit:SMT_257|3end_predicted_integral_membrane_protein_195132..195282_POSITIVE 219 181 142 43 7 smit:SMT_1810|3end_hypothetical_protein_1785598..1785748_POSITIVE 219 46 8 39 7 smit:SMT_1176|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1127662..1127812_NEGATIVE 211 50 6 65 22 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 210 347 302 101 52 smit:SMT_688|3end_carbamoyl-phosphate_synthase_small_chain_599576..599726_NEGATIVE 209 340 301 70 32 smit:SMT_361|3end_hypothetical_protein_296293..296443_POSITIVE 208 54 16 77 36 smit:SMT_2050|3end_K03712_MarR_family_transcriptional_regulator_1959539..1959689_NEGATIVE 208 395 355 78 29 smit:SMT_777|3end_hypothetical_protein_686618..686768_NEGATIVE 207 234 193 119 76 smit:SMT_1054|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_993687..993837_NEGATIVE 207 249 203 88 32 smit:SMT_707|3end_hypothetical_protein_predicted_by_Glimmer/Critica_616239..616389_NEGATIVE 204 50 3 141 96 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE