Origin IGS: tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta .........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 taagggatctcacaatgcattatttaaacaaaaaattgcctagattatacaggattttgatcgttctaacagcttgaaaatagcaagtgcggtgaaaatttgaagaatttataacggttttcttttcaagataacgattctataaaaatcggcgaaaaaaggggcacaagatcccttcta Mask Tandem Repeat Region ================================================ tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta Find is-nt database================================================ Query_seq: AA02103:AA02105|AA02103:AA02105:D-alanyl-D-alanine-endopeptidase; penicillin-binding protein 7:killing protein:->->:1431845..1432024 180 tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02103:AA02105|AA02103:AA02105:D-alanyl-D-alanine-endopeptidase; penicillin-binding protein 7:killing protein:->->:1431845..1432024 180 tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02103:AA02105|AA02103:AA02105:D-alanyl-D-alanine-endopeptidase; penicillin-binding protein 7:killing protein:->->:1431845..1432024 180 tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 69 End: 158 .................................................................... M N S S N F H R T C Y F Q A V R T I K I L Y N L G N F L F K ...................... tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA02103:AA02105|AA02103:AA02105:D-alanyl-D-alanine-endopeptidase; penicillin-binding protein 7:killing protein:->->:1431845..1432024 180 tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: aact_AA02103_AA02105|D-alanyl-D-alanine-endopeptidase; penicillin-binding protein 7:killing protein|POSITIVE:POSITIVE|[1431845,1432024]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta tagaagggatcttgtgccccttttttcgccgatttttatagaatcgttatcttgaaaagaaaaccgttataaattcttcaaattttcaccgcacttgctattttcaagctgttagaacgatcaaaatcctgtataatctaggcaattttttgtttaaataatgcattgtgagatccctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAGGGAUCUUGUGCCCCUUUUUUCGCCGAUUUUUAUAGAAUCGUUAUCUUGAAAAGAAAACCGUUAUAAAUUCUUCAAAUUUUCACCGCACUUGCUAUUUUCAAGCUGUUAGAACGAUCAAAAUCCUGUAUAAUCUAGGCAAUUUUUUGUUUAAAUAAUGCAUUGUGAGAUCCCUUA ...(((((((((..(...............((((((....((.(((((..(((((((((((((...................)))))...((....))..)))))))).......))))))))))))).(((((.((.(((((((....))))))).)).)))))..)..))))))))). (-36.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGGAUCUCACAAUGCAUUAUUUAAACAAAAAAUUGCCUAGAUUAUACAGGAUUUUGAUCGUUCUAACAGCUUGAAAAUAGCAAGUGCGGUGAAAAUUUGAAGAAUUUAUAACGGUUUUCUUUUCAAGAUAACGAUUCUAUAAAAAUCGGCGAAAAAAGGGGCACAAGAUCCCUUCUA .(((((((((.....(((.............(((((((..((((((.....(((((((.(((((.......(((((.......)))))))))).)))))))....))))))...)))))))(((((...(....(((((.......))))).)...)))))..)))..)))))))))... (-36.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 113 73 210 156 aact:AA01635|5end_ribonucleoside_diphosphate_reductase,_beta_chain_1104615..1104845_POSITIVE 321 30 3 224 192 aact:AA02415|5end_hypothetical_protein_1658443..1658673_POSITIVE 306 55 12 80 35 aact:AA02228|5end_regulatory_protein,_sorC_family_1514981..1515211_POSITIVE 297 123 83 155 123 aact:AA02695|5end_hydrogenase-3_component_G_1878565..1878795_POSITIVE 293 126 83 227 191 aact:AA00460|5end_ATP-dependent_ClpY-related_protease;_heat_shock_protein_321023..321253_POSITIVE 293 126 83 55 19 aact:AA00459|5end_hypothetical_protein_320851..321081_POSITIVE 284 30 6 216 196 aact:AA01168|5end_6-phosphogluconolactonase_801243..801473_POSITIVE 277 129 85 103 60 aact:AA00813|5end_hypothetical_protein_558807..559037_POSITIVE 272 121 88 70 29 aact:AA01908|5end_conserved_hypothetical_protein_1287068..1287298_POSITIVE 269 46 6 62 28 aact:AA01758|5end_hydrogenase_isoenzymes_nickel_incorporation_protein_1187839..1188069_POSITIVE 267 129 87 62 17 aact:AA02821|5end_ribosomal-protein-alanine_acetyltransferase_1982255..1982485_POSITIVE 265 100 61 126 79 aact:AA02836|5end_colicin_transport_protein_1991777..1992007_POSITIVE 265 100 61 50 3 aact:AA02835|5end_hypothetical_protein_1991701..1991931_POSITIVE 265 129 83 172 124 aact:AA01441|5end_tRNA/rRNA_methylase_966490..966720_POSITIVE 265 123 86 91 61 aact:AA01188|5end_conserved_hypothetical_protein_813912..814142_POSITIVE 262 116 71 180 133 aact:AA00194|5end_oxygen-independent_coproporphyrinogen_III_oxidase_135545..135775_POSITIVE 260 130 83 173 136 aact:AA01640|5end_restriction_enzyme_type_I_helicase_subunit_1109230..1109460_POSITIVE 260 130 83 79 42 aact:AA01639|5end_hypothetical_protein_1109136..1109366_POSITIVE 260 96 51 206 153 aact:AA01621|5end_replicative_DNA_helicase_1095647..1095877_POSITIVE 260 96 51 72 19 aact:AA01620|5end_hypothetical_protein_1095513..1095743_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 110 64 149 104 aact:AA02693|3end_hydrogenase-4_component_H_1878645..1878795_POSITIVE 277 129 85 66 23 aact:AA00812|3end_ATPase_(PP-loop_superfamily),_confers_aluminum_resistance_558850..559000_POSITIVE 267 129 87 49 4 aact:AA02819|3end_DNA_polymerase_III,_psi_subunit_1982322..1982472_POSITIVE 265 100 61 145 98 aact:AA02835|3end_hypothetical_protein_1991876..1992026_POSITIVE 265 129 83 100 52 aact:AA01439|3end_probable_ferredoxin_(fdx-2)_966498..966648_POSITIVE 265 123 86 91 61 aact:AA01187|3end_conserved_hypothetical_protein_813992..814142_POSITIVE 262 116 71 100 53 aact:AA00191|3end_conserved_hypothetical_protein_(possible_acetyltransferase,_GNAT_family)_135545..135695_POSITIVE 260 96 51 57 4 aact:AA01619|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthase)_1095578..1095728_POSITIVE 258 130 81 112 53 aact:AA02813|3end_hypothetical_protein_1980298..1980448_POSITIVE 257 128 88 74 36 aact:AA02937|3end_conserved_hypothetical_protein_2056947..2057097_POSITIVE 255 99 64 148 114 aact:AA01092|3end_hypothetical_protein_756361..756511_POSITIVE 255 118 73 48 5 aact:AA00809|3end_possible_oxidoreductase_555435..555585_POSITIVE 254 129 83 102 45 aact:AA00234|3end_collagen_adhesin_168641..168791_POSITIVE 252 138 91 125 62 aact:AA01660|3end_hypothetical_protein_1125282..1125432_POSITIVE 251 49 2 65 19 aact:AA00894|3end_selenium_transferase_(Cysteinyl-tRNA(Sec)_selenium_transferase)_621350..621500_POSITIVE 248 35 12 70 40 aact:AA00528|3end_conserved_hypothetical_protein_361703..361853_POSITIVE 245 113 80 92 55 aact:AA02076|3end_conserved_hypothetical_protein_1411094..1411244_POSITIVE 244 99 51 118 62 aact:AA02519|3end_DNA_gyrase_A_1752612..1752762_POSITIVE 243 128 89 94 52 aact:AA02075|3end_conserved_hypothetical_protein_1409979..1410129_POSITIVE 243 118 82 109 66 aact:AA01145|3end_glycyl-tRNA_synthetase_alpha_subunit_784460..784610_POSITIVE