Origin IGS: gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcctcataagcaagaggcgaagatatttccccgcctcactttctcatattcttactcttagtatagcacgtttgccaacttatgtaaagcaaaagcacttatacagcctgatttcaggctatttc Mask Tandem Repeat Region ================================================ gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Find is-nt database================================================ Query_seq: SMT_357:SMT_358|SMT_357:SMT_358:tRNA (guanine-N7-)-methyltransferase:hypothetical protein:->->:293961..294086 126 gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_357:SMT_358|SMT_357:SMT_358:tRNA (guanine-N7-)-methyltransferase:hypothetical protein:->->:293961..294086 126 gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_357:SMT_358|SMT_357:SMT_358:tRNA (guanine-N7-)-methyltransferase:hypothetical protein:->->:293961..294086 126 gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 1 End: 120 F Y G S I L S Y L H K Q K V Y T P L R A I S L T L I H S L S A P F Y R R R K S M ...... gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag 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: 84 Start: 37 End: 66 ....................................CTTTACATAAGTTGGCAAACGTGCTATACT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_357:SMT_358|SMT_357:SMT_358:tRNA (guanine-N7-)-methyltransferase:hypothetical protein:->->:293961..294086 126 gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: smit_SMT_357_SMT_358|tRNA (guanine-N7-)-methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[293961,294086]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag gaaatagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Inter-species Hit: Count: 3 Min: 4 Max: 126 Len: 123 Subject: NC_008533_SPD_0477_SPD_0478|tRNA (guanine-N(7)-)-methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[487035,487159]|125 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 123 Query Start:4 Query End:126 Subject Strand: POSITIVE Subject Start: 4 Subject End: 125 ...atagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag ...atagcctaaaattaggctgtacaagtgcttttgctttacataagttggcaaacgtgctatactgatagtaagaatatga-aaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Subject: NC_003098_spr0476_spr0477|tRNA (guanine-N(7)-)-methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[479505,479629]|125 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 123 Query Start:4 Query End:126 Subject Strand: POSITIVE Subject Start: 4 Subject End: 125 ...atagcctgaaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag ...atagcctaaaattaggctgtacaagtgcttttgctttacataagttggcaaacgtgctatactgatagtaagaatatga-aaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Subject: NC_003028_SP_0550_SP_0552|tRNA (guanine-N(7)-)-methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[520716,520840]|125 HSP 1 e-value: 7.0E-45 bit: 180.0 Len: 115 Query Start:12 Query End:126 Subject Strand: POSITIVE Subject Start: 12 Subject End: 125 ...........aaatcaggctgtataagtgcttttgctttacataagttggcaaacgtgctatactaagagtaagaatatgagaaagtgaggcggggaaatatcttcgcctcttgcttatgaggag ...........aaattaggctgtacaagtgcttttgctttacataagttggcaaacgtgctatactgatagtaagaatatga-aaagtgaggcggggaaatatcttcgcctcttgcttatgaggag Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGCCUGAAAUCAGGCUGUAUAAGUGCUUUUGCUUUACAUAAGUUGGCAAACGUGCUAUACUAAGAGUAAGAAUAUGAGAAAGUGAGGCGGGGAAAUAUCUUCGCCUCUUGCUUAUGAGGAG ((((((((....))))))))...((..(.((((((..((....)).)))))).)..))................((((((.....((((((((((....))))))))))...))))))..... (-43.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUCAUAAGCAAGAGGCGAAGAUAUUUCCCCGCCUCACUUUCUCAUAUUCUUACUCUUAGUAUAGCACGUUUGCCAACUUAUGUAAAGCAAAAGCACUUAUACAGCCUGAUUUCAGGCUAU ......(((((...((((((..((....))..))))))............................((...(((((..((....))...))))).)).)))))..((((((....)))))).. (-30.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 108 65 36 1 smit:SMT_1123|5end_hypothetical_protein_1059292..1059522_POSITIVE 283 110 79 143 113 smit:SMT_1806|5end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781229..1781459_POSITIVE 283 110 79 143 113 smit:SMT_1635|5end_putative_N-acetyldiaminopimelate_deacetylase_1621426..1621656_POSITIVE 281 57 13 227 188 smit:SMT_2008|5end_K07485_transposase_1928662..1928892_NEGATIVE 281 57 13 96 57 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 281 57 13 190 151 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 281 57 13 190 151 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 281 57 13 225 186 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 281 57 13 190 151 smit:SMT_1690|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1674779..1675009_NEGATIVE 281 57 13 190 151 smit:SMT_779|5end_ribonuclease_BN,_putative_688530..688760_NEGATIVE 281 57 13 111 72 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 281 57 13 190 151 smit:SMT_388|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_321172..321402_POSITIVE 281 57 13 164 125 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 280 68 22 151 110 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 265 95 53 209 166 smit:SMT_1412|5end_hypothetical_protein_1395522..1395752_POSITIVE 264 118 82 46 11 smit:SMT_501|5end_ABC_transporter,_ATP-binding_protein_433227..433457_POSITIVE 263 112 72 86 43 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 263 58 14 176 123 smit:SMT_156|5end_hypothetical_protein_102869..103099_POSITIVE 262 70 25 202 154 smit:SMT_776|5end_hypothetical_protein_686202..686432_POSITIVE 261 50 2 50 10 smit:SMT_225|5end_pullulanase_163529..163759_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 107 64 105 56 smit:SMT_1144|3end_K02026_multiple_sugar_transport_system_permease_protein_1089144..1089294_POSITIVE 294 50 9 144 101 smit:SMT_1246|3end_ISSag9,_transposase_1205938..1206088_NEGATIVE 293 119 78 87 51 smit:SMT_1097|3end_alcohol_dehydrogenase_/_acetaldehyde_dehydrogenase_1038697..1038847_NEGATIVE 283 110 79 75 45 smit:SMT_1805|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1781241..1781391_POSITIVE 283 110 79 75 45 smit:SMT_1634|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621438..1621588_POSITIVE 282 40 1 109 68 smit:SMT_357|3end_tRNA_(guanine-N7-)-methyltransferase_293900..294050_POSITIVE 281 57 13 61 22 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 281 57 13 56 17 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE 280 68 22 149 108 smit:SMT_1693|3end_dimethyladenosine_transferase_1676752..1676902_POSITIVE 270 60 11 65 8 smit:SMT_1867|3end_peptide_chain_release_factor_1_1827910..1828060_NEGATIVE 269 115 79 60 18 smit:SMT_1300|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1262614..1262764_NEGATIVE 264 119 77 145 105 smit:SMT_1129|3end_hypothetical_protein_1063303..1063453_NEGATIVE 264 118 82 44 9 smit:SMT_500|3end_hypothetical_protein_433305..433455_POSITIVE 259 108 66 88 49 smit:SMT_135|3end_hypothetical_protein_86178..86328_NEGATIVE 251 58 13 51 8 smit:SMT_987|3end_N-acetylmannosamine_kinase_/_transcriptional_regulator_931655..931805_NEGATIVE 251 108 61 92 33 smit:SMT_839|3end_ABC_transporter,_ATP-binding_protein_784194..784344_NEGATIVE 243 108 61 79 31 smit:SMT_1046|3end_chaperonin_GroEL_987638..987788_NEGATIVE 243 114 76 82 43 smit:SMT_141|3end_K03495_glucose_inhibited_division_protein_A_93401..93551_POSITIVE 240 118 78 47 12 smit:SMT_2068|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974183..1974333_NEGATIVE 239 35 1 117 85 smit:SMT_1642|3end_K03497_chromosome_partitioning_protein,_ParB_family_1628493..1628643_NEGATIVE