Origin IGS: cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattaacagcatttttaactcgagttataaaaaccgtgaatcttcccaggctcacggttttattttctctcaatcttatcagttagactcatatttcgttcacaataagaggcagaatactcg Mask Tandem Repeat Region ================================================ cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta Find is-nt database================================================ Query_seq: AA02398:AA02399|AA02398:AA02399:DNA primase:30S ribosomal protein S21:->->:1650916..1651039 124 cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02398:AA02399|AA02398:AA02399:DNA primase:30S ribosomal protein S21:->->:1650916..1651039 124 cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02398:AA02399|AA02398:AA02399:DNA primase:30S ribosomal protein S21:->->:1650916..1651039 124 cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 3 End: 122 .. T N Q R K N H V F Y S D L Q Y S Q S F I F G H A Q S S E R N K Y S S N F I S N M .. cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta 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: 82 Start: 93 End: 122 ............................................................................................ATTAACAGCATTTTTAACTCGAGTTATAAA.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 84 HP_score: -7.5 Tail_Score: -4.56961 Start: 62 End: 95 Full_Region: tttaactcgagttat aaaaaccgtgaatct tccc aggctcacggtttta ttttctctcaatctt .............................................................aaaaaccgtgaatcttcccaggctcacggtttta............................. TransTerm Strand: + Conf: 83 HP_score: -7.4 Tail_Score: -4.87665 Start: 67 End: 90 Full_Region: TGAGAGAAAATAAAA CCGTGAGCCT GGGA AGATTCACGG TTTTTATAACTCGAG ..................................................................CCGTGAGCCTGGGAAGATTCACGG.................................. Find igs database================================================ Query_seq: AA02398:AA02399|AA02398:AA02399:DNA primase:30S ribosomal protein S21:->->:1650916..1651039 124 cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: aact_AA02398_AA02399|DNA primase:30S ribosomal protein S21|POSITIVE:POSITIVE|[1650916,1651039]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta cgagtattctgcctcttattgtgaacgaaatatgagtctaactgataagattgagagaaaataaaaccgtgagcctgggaagattcacggtttttataactcgagttaaaaatgctgttaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAGUAUUCUGCCUCUUAUUGUGAACGAAAUAUGAGUCUAACUGAUAAGAUUGAGAGAAAAUAAAACCGUGAGCCUGGGAAGAUUCACGGUUUUUAUAACUCGAGUUAAAAAUGCUGUUAAUUA (((((.......(((((((((....)))..(((.((.....)).)))....)))))).....((((((((((..((....))..))))))))))....)))))..................... (-28.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUAACAGCAUUUUUAACUCGAGUUAUAAAAACCGUGAAUCUUCCCAGGCUCACGGUUUUAUUUUCUCUCAAUCUUAUCAGUUAGACUCAUAUUUCGUUCACAAUAAGAGGCAGAAUACUCG .....................(((((....((((((((((..((....))..))))))))))......(((...((((((......((........)).......))))))...)))..))))) (-24.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 97 65 228 194 aact:AA01199|5end_conserved_hypothetical_protein_821984..822214_POSITIVE 263 91 54 196 146 aact:AA02001|5end_conserved_hypothetical_protein_1359842..1360072_POSITIVE 257 90 48 174 114 aact:AA00383|5end_chloride_channel_protein_258894..259124_POSITIVE 256 45 1 190 136 aact:AA00993|5end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694488..694718_POSITIVE 255 116 76 74 35 aact:AA01097|5end_conserved_hypothetical_protein_757189..757419_POSITIVE 252 107 67 75 32 aact:AA01747|5end_single-stranded-DNA-specific_exonuclease_1181359..1181589_POSITIVE 252 108 67 71 28 aact:AA01445|5end_hypothetical_protein_969899..970129_POSITIVE 251 105 66 135 95 aact:AA00163|5end_type_IV_prepilin_peptidase;_type_II_secretion_pathway_related_protein_116006..116236_POSITIVE 247 50 4 50 5 aact:AA00398|5end_protein-tyrosine-phosphatase_(PTPase)_267447..267677_POSITIVE 245 90 42 86 42 aact:AA01050|5end_iron(III)_ABC_transporter,_permease_protein_730501..730731_POSITIVE 242 100 54 129 82 aact:AA01153|5end_sec-independent_protein_translocase_790166..790396_POSITIVE 242 45 1 98 54 aact:AA00464|5end_conserved_hypothetical_protein_323912..324142_POSITIVE 239 120 75 93 53 aact:AA01956|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1322436..1322666_POSITIVE 239 93 62 48 16 aact:AA00003|5end_DNA_replication_and_repair_protein_2337..2567_POSITIVE 237 120 73 178 124 aact:AA00915|5end_xanthine-guanine_phosphoribosyltransferase_629610..629840_POSITIVE 236 50 9 169 126 aact:AA03008|5end_GTP-binding_protein_era_homolog_(GTPase)_2100087..2100317_POSITIVE 234 90 49 161 112 aact:AA01507|5end_conserved_hypothetical_protein_1012433..1012663_POSITIVE 232 38 8 158 130 aact:AA00113|5end_uracil_phosphoribosyltransferase_81286..81516_POSITIVE 228 78 33 161 114 aact:AA01259|5end_protoporphyrinogen_oxidase_854354..854584_POSITIVE 228 90 41 152 90 aact:AA00844|5end_cell_division_protein_I;_penicillin_binding_protein_2X_582802..583032_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 90 41 122 66 aact:AA02541|3end_conserved_hypothetical_protein_1772644..1772794_POSITIVE 263 91 54 75 25 aact:AA02000|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_1359801..1359951_POSITIVE 261 119 73 110 66 aact:AA01598|3end_conserved_hypothetical_protein_1079966..1080116_POSITIVE 257 90 48 85 25 aact:AA00382|3end_hypothetical_protein_258885..259035_POSITIVE 255 116 76 87 48 aact:AA01096|3end_conserved_hypothetical_protei_757282..757432_POSITIVE 251 105 66 135 95 aact:AA00162|3end_pilin_C_biogenesis_protein/protein_transport_protein_116086..116236_POSITIVE 249 120 76 124 79 aact:AA02416|3end_conserved_hypothetical_protein_1659578..1659728_POSITIVE 242 100 54 88 41 aact:AA01152|3end_sec-independent_protein_translocase_protein_790205..790355_POSITIVE 239 93 62 41 9 aact:AA00002|3end_DNA_polymerase_III,_beta_subunit_2410..2560_POSITIVE 237 120 73 63 9 aact:AA00914|3end_aminoacyl-histidine_dipeptidase;_Beta-alanyl-histidine_dipeptidase_629575..629725_POSITIVE 234 90 49 142 93 aact:AA01506|3end_protein-export_protein_1012494..1012644_POSITIVE 234 118 71 125 73 aact:AA01155|3end_hypothetical_protein_791411..791561_POSITIVE 232 38 8 31 3 aact:AA00112|3end_uracil_permease_81239..81389_POSITIVE 231 120 73 139 88 aact:AA02959|3end_pyrroline-5-carboxylate_(P5C)_reductase_2070976..2071126_POSITIVE 228 90 41 131 69 aact:AA00841|3end_UDP-MurNAc-tripeptide_synthetase_582861..583011_POSITIVE 226 90 49 119 86 aact:AA00160|3end_pilA-like_biogenesis_protein_/_prepilin_peptidase_dependent_proteinD_113434..113584_POSITIVE 225 90 44 80 24 aact:AA00168|3end_possible_sigma_54_modulation_protein_120240..120390_POSITIVE 224 96 59 68 37 aact:AA02554|3end_conserved_hypothetical_protein_1780486..1780636_POSITIVE 223 91 55 56 15 aact:AA01703|3end_L-ribulose-phosphate_4-epimerase_1156161..1156311_POSITIVE 221 106 61 144 101 aact:AA02411|3end_cysteine_synthetase_1657504..1657654_POSITIVE