Origin IGS: gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggatttcctcactttatctattataccataaaaggtaaactttcaataaaatagccactttcttccttattctactaggctattgcccaagtttgtgatacaatagttagaaacaatatttttaaaaaggagaaaagacac Mask Tandem Repeat Region ================================================ gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc Find is-nt database================================================ Query_seq: SMT_1802:SMT_1803|SMT_1802:SMT_1803:tyrosyl-tRNA synthetase:K03693 penicillin binding protein:<-->:1776803..1776943 141 gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1802:SMT_1803|SMT_1802:SMT_1803:tyrosyl-tRNA synthetase:K03693 penicillin binding protein:<-->:1776803..1776943 141 gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1802:SMT_1803|SMT_1802:SMT_1803:tyrosyl-tRNA synthetase:K03693 penicillin binding protein:<-->:1776803..1776943 141 gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc Predict ORF larger than 30AA ================================================ gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc 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: 38 End: 67 .....................................CTAGGCTATTGCCCAAGTTTGTGATACAAT.......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1802:SMT_1803|SMT_1802:SMT_1803:tyrosyl-tRNA synthetase:K03693 penicillin binding protein:<-->:1776803..1776943 141 gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: smit_SMT_1802_SMT_1803|tyrosyl-tRNA synthetase:K03693 penicillin binding protein|NEGATIVE:POSITIVE|[1776803,1776943]|141 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc Inter-species Hit: Count: 3 Min: 1 Max: 141 Len: 141 Subject: NC_008533_SPD_1925_SPD_1926|penicillin-binding protein 1B:tyrosyl-tRNA synthetase|NEGATIVE:POSITIVE|[1896034,1896174]|141 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 141 Query Start:1 Query End:141 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 141 gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc gtgttttttctcctttttaaaattattgtttctacctattgtatcacaaacttgggcaatagcctagcagaatagggaagaaagtggctattttattgaaaatttcccttttgtggtataatagataaagtgaggaaatcc Subject: NC_003098_spr1909_spr1910|Penicillin-binding protein 1b:tyrosyl-tRNA synthetase|NEGATIVE:POSITIVE|[1888502,1888642]|141 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 141 Query Start:1 Query End:141 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 141 gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc gtgttttttctcctttttaaaattattgtttctacctattgtatcacaaacttgggcaatagcctagcagaatagggaagaaagtggctattttattgaaaatttcccttttgtggtataatagataaagtgaggaaatcc Subject: NC_003028_SP_2099_SP_2100|penicillin-binding protein 1B:tyrosyl-tRNA synthetase|NEGATIVE:POSITIVE|[2009167,2009307]|141 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 141 Query Start:1 Query End:141 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 141 gtgtcttttctcctttttaaaaatattgtttctaactattgtatcacaaacttgggcaatagcctagtagaataaggaagaaagtggctattttattgaaagtttaccttttatggtataatagataaagtgaggaaatcc gtgttttttctcctttttaaaattattgtttctacctattgtatcacaaacttgggcaatagcctagcagaatagggaagaaagtggctattttattgaaaatttcccttttgtggtataatagataaagtgaggaaatcc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUCUUUUCUCCUUUUUAAAAAUAUUGUUUCUAACUAUUGUAUCACAAACUUGGGCAAUAGCCUAGUAGAAUAAGGAAGAAAGUGGCUAUUUUAUUGAAAGUUUACCUUUUAUGGUAUAAUAGAUAAAGUGAGGAAAUCC .....(((((((((((...................(((((((((((...(((.((((....)))))))...........(((((.(...(((((....)))))...)))))).)))))))))))..)))).)))))))... (-25.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUUUCCUCACUUUAUCUAUUAUACCAUAAAAGGUAAACUUUCAAUAAAAUAGCCACUUUCUUCCUUAUUCUACUAGGCUAUUGCCCAAGUUUGUGAUACAAUAGUUAGAAACAAUAUUUUUAAAAAGGAGAAAAGACAC ((....))....(((((((.((((...)))).)))))))..................((((..(((((.........(((....)))...((((.((((......)))).))))............)))))..)))).... (-23.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 881 90 41 181 132 smit:SMT_1802|5end_tyrosyl-tRNA_synthetase_1776712..1776942_NEGATIVE 292 88 47 187 145 smit:SMT_890|5end_K02029_polar_amino_acid_transport_system_permease_protein_836953..837183_POSITIVE 283 48 2 134 83 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 251 87 52 56 14 smit:SMT_2053|5end_hypothetical_membrane_associated_protein_1964422..1964652_NEGATIVE 243 46 2 79 39 smit:SMT_846|5end_hypothetical_protein_792769..792999_NEGATIVE 242 78 31 62 3 smit:SMT_754|5end_3-dehydroquinate_synthase_659044..659274_NEGATIVE 240 79 31 49 3 smit:SMT_1568|5end_putative_transketolase_C-terminal_section_1560122..1560352_POSITIVE 239 59 25 69 27 smit:SMT_2098|5end_similar_to_CDP-ribitol_pyrophosphorylase_1991376..1991606_POSITIVE 236 49 6 144 95 smit:SMT_683|5end_similar_to_CDP-ribitol_pyrophosphorylase_592572..592802_NEGATIVE 232 46 6 132 93 smit:SMT_1898|5end_aminotransferase_(class_V),_putative_1849929..1850159_NEGATIVE 228 90 50 189 145 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 227 64 26 164 127 smit:SMT_1134|5end_glutamyl-tRNA_synthetase_1076464..1076694_NEGATIVE 224 112 72 189 150 smit:SMT_2018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1936760..1936990_POSITIVE 224 112 72 189 150 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 221 87 44 72 15 smit:SMT_326|5end_K02029_polar_amino_acid_transport_system_permease_protein_263864..264094_NEGATIVE 220 56 13 133 96 smit:SMT_746|5end_LPS_biosynthesis_protein_651222..651452_NEGATIVE 218 68 31 220 178 smit:SMT_1820|5end_cation_transporter_CorA_family_1793600..1793830_POSITIVE 218 46 2 138 92 smit:SMT_1258|5end_acetolactate_synthase_large_subunit_1224866..1225096_NEGATIVE 218 55 11 134 98 smit:SMT_652|5end_transporter,_putative_563215..563445_NEGATIVE 218 45 1 128 73 smit:SMT_505|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_437106..437336_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 46 1 85 28 smit:SMT_120|3end_hypothetical_protein_72943..73093_POSITIVE 240 79 31 52 6 smit:SMT_1567|3end_transketolase,_N-terminal_subunit_1560205..1560355_POSITIVE 236 89 46 74 20 smit:SMT_1524|3end_peptidase_T_1505867..1506017_POSITIVE 233 98 52 71 21 smit:SMT_1878|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1835228..1835378_NEGATIVE 230 94 51 69 17 smit:SMT_1860|3end_hypothetical_protein_1822611..1822761_NEGATIVE 218 68 31 95 53 smit:SMT_1819|3end_K03442_small_conductance_mechanosensitive_ion_channel,_MscS_family_1793555..1793705_POSITIVE 218 55 11 57 21 smit:SMT_653|3end_positive_transcriptional_regulator_MutR_family_563292..563442_NEGATIVE 217 64 29 36 3 smit:SMT_1135|3end_glucose-6-phosphate_isomerase_1076592..1076742_NEGATIVE 217 70 29 148 109 smit:SMT_436|3end_amidase_related_to_nicotinamidase_377575..377725_NEGATIVE 209 60 14 47 1 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 208 99 53 70 30 smit:SMT_935|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_888749..888899_POSITIVE 207 55 12 54 12 smit:SMT_331|3end_endo-beta-N-acetylglucosaminidase_271415..271565_POSITIVE 205 70 34 140 97 smit:SMT_807|3end_hypothetical_protein_predicted_by_Glimmer/Critica_716708..716858_NEGATIVE 203 126 81 149 104 smit:SMT_1333|3end_glycosyltransferase_1307592..1307742_NEGATIVE 202 88 63 35 1 smit:SMT_1367|3end_K02237_competence_protein_ComEA_1346872..1347022_NEGATIVE 201 69 28 60 15 smit:SMT_356|3end_hypothetical_protein_293268..293418_POSITIVE 200 87 50 65 21 smit:SMT_1046|3end_chaperonin_GroEL_987638..987788_NEGATIVE 199 50 1 42 3 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 197 91 52 111 67 smit:SMT_479|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_415604..415754_NEGATIVE 197 100 51 52 6 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE