Origin IGS: tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa .........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 tttgtttttctcctcttactagtagtttgcaagttgcacttgctagttaatgattgagctaggctcagatagtattgatacattcaaatgagaaaactcttatttgaacacgagctacaacctgtgcaaaaaagataaatttgttttggagcatcgctcctacaccaaatttcctatttttgctgtggttgttacgctcttcgtatcatgata Mask Tandem Repeat Region ================================================ tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa Find is-nt database================================================ Query_seq: SMT_183:SMT_184|SMT_183:SMT_184:30S ribosomal protein S14:30S ribosomal protein S8:->->:121340..121552 213 tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_183:SMT_184|SMT_183:SMT_184:30S ribosomal protein S14:30S ribosomal protein S8:->->:121340..121552 213 tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_183:SMT_184|SMT_183:SMT_184:30S ribosomal protein S14:30S ribosomal protein S8:->->:121340..121552 213 tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 6 End: 110 ..... * S V F L T V V V A F I P F K T Y S R H E L V F K D K K C L N Y S T N M ....................................................................................................... tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa 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================================================ tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_183:SMT_184|SMT_183:SMT_184:30S ribosomal protein S14:30S ribosomal protein S8:->->:121340..121552 213 tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa Intra-Species Hit: Count: 1 Min: 1 Max: 213 Len: 213 Subject: smit_SMT_183_SMT_184|30S ribosomal protein S14:30S ribosomal protein S8|POSITIVE:POSITIVE|[121340,121552]|213 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa tatcatgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaataagagttttctcatttgaatgtatcaatactatctgagcctagctcaatcattaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa Inter-species Hit: Count: 3 Min: 4 Max: 213 Len: 210 Subject: NC_008533_SPD_0206_SPD_0207|ribosomal protein S14:ribosomal protein S8|POSITIVE:POSITIVE|[202453,202736]|284 HSP 1 e-value: 9.0E-21 bit: 101.0 Len: 51 Query Start:163 Query End:213 Subject Strand: POSITIVE Subject Start: 234 Subject End: 284 ..................................................................................................................................................................attaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa ..................................................................................................................................................................attaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 109 Query Start:4 Query End:112 Subject Strand: NEGATIVE Subject Start: 124 Subject End: 232 ...catgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaat..................................................................................................... ...catgatacaaagagcgtaacagcacgagcaaaaatagacaattgaatgcagaagcaatgctccaaagcaaattggtcttttttgccaaagctgtagctcgtgttcaaat..................................................................................................... Subject: NC_003098_spr0202_spr0203|30S Ribosomal protein S14:30S ribosomal protein S8|POSITIVE:POSITIVE|[202453,202736]|284 HSP 1 e-value: 9.0E-21 bit: 101.0 Len: 51 Query Start:163 Query End:213 Subject Strand: POSITIVE Subject Start: 234 Subject End: 284 ..................................................................................................................................................................attaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa ..................................................................................................................................................................attaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 109 Query Start:4 Query End:112 Subject Strand: NEGATIVE Subject Start: 124 Subject End: 232 ...catgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaat..................................................................................................... ...catgatacaaagagcgtaacagcacgagcaaaaatagacaattgaatgcagaagcaatgctccaaagcaaattggtcttttttgccaaagctgtagctcgtgttcaaat..................................................................................................... Subject: NC_003028_SP_0223_SP_0224|hypothetical protein:30S ribosomal protein S8|NEGATIVE:POSITIVE|[200033,200227]|195 HSP 1 e-value: 9.0E-21 bit: 101.0 Len: 51 Query Start:163 Query End:213 Subject Strand: POSITIVE Subject Start: 145 Subject End: 195 ..................................................................................................................................................................attaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa ..................................................................................................................................................................attaactagcaagtgcaacttgcaaactactagtaagaggagaaaaacaaa HSP 2 e-value: 5.0E-10 bit: 65.9 Len: 109 Query Start:4 Query End:112 Subject Strand: NEGATIVE Subject Start: 35 Subject End: 143 ...catgatacgaagagcgtaacaaccacagcaaaaataggaaatttggtgtaggagcgatgctccaaaacaaatttatcttttttgcacaggttgtagctcgtgttcaaat..................................................................................................... ...catgatacaaagagcgtaacagcacgagcaaaaatagacaatttaatgcagaagcaatgctccaaagcaaattggtcttttttgccaaagctgtagctcgtgttcaaat..................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUGAUACGAAGAGCGUAACAACCACAGCAAAAAUAGGAAAUUUGGUGUAGGAGCGAUGCUCCAAAACAAAUUUAUCUUUUUUGCACAGGUUGUAGCUCGUGUUCAAAUAAGAGUUUUCUCAUUUGAAUGUAUCAAUACUAUCUGAGCCUAGCUCAAUCAUUAACUAGCAAGUGCAACUUGCAAACUACUAGUAAGAGGAGAAAAACAAA ..((((((...((((...((((((...(((((((.((((((((((.....(((((...)))))....))))))).))))))))))...)))))).))))..((((((((.((......)).)))))))))))))).(((((..(((((...)))))...........(((((.....))))).......)))))................ (-61.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUUUUUCUCCUCUUACUAGUAGUUUGCAAGUUGCACUUGCUAGUUAAUGAUUGAGCUAGGCUCAGAUAGUAUUGAUACAUUCAAAUGAGAAAACUCUUAUUUGAACACGAGCUACAACCUGUGCAAAAAAGAUAAAUUUGUUUUGGAGCAUCGCUCCUACACCAAAUUUCCUAUUUUUGCUGUGGUUGUUACGCUCUUCGUAUCAUG ...((((..(((.((..((((((((..(((.....))).))))))))....))..)))..))))...........((((((.(((((((((((....)))))))))))...((((.((((((...(((((((....(((((((....(((((...))))).....)))))))....)))))))...))))))...))))...)))))).. (-64.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 531 80 31 172 123 smit:SMT_342|5end_chaperone_protein_DnaJ_281800..282030_POSITIVE 442 50 2 145 97 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 389 80 31 176 127 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 300 64 26 220 179 smit:SMT_2127|5end_exodeoxyribonuclease_V_alpha_chain_2009306..2009536_POSITIVE 295 64 23 97 48 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 270 190 141 106 59 smit:SMT_2159|5end_cell_division_protein_FtsA_2032010..2032240_POSITIVE 270 201 164 76 44 smit:SMT_1209|5end_choline_binding_protein_PcpA_1170972..1171202_NEGATIVE 268 98 58 152 104 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 267 154 111 53 13 smit:SMT_374|5end_hypothetical_protein_309788..310018_POSITIVE 261 80 31 207 159 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 261 80 31 79 31 smit:SMT_545|5end_hypothetical_protein_predicted_by_Glimmer/Critica_461249..461479_POSITIVE 261 162 121 127 89 smit:SMT_313|5end_3R-hydroxymyristoyl_ACP_dehydrase_253843..254073_POSITIVE 258 64 23 192 155 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 257 160 113 68 19 smit:SMT_1204|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1164723..1164953_NEGATIVE 257 60 11 141 81 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 254 89 45 228 176 smit:SMT_898|5end_polyribonucleotide_nucleotidyltransferase_846861..847091_NEGATIVE 253 98 61 52 12 smit:SMT_842|5end_hypothetical_protein_789262..789492_NEGATIVE 253 60 13 55 5 smit:SMT_610|5end_hypothetical_protein_521659..521889_POSITIVE 251 31 2 63 27 smit:SMT_1620|5end_hypothetical_protein_1607240..1607470_NEGATIVE 251 188 141 65 8 smit:SMT_1208|5end_choline_binding_protein_PcpA_1169690..1169920_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 99 51 76 25 smit:SMT_183|3end_30S_ribosomal_protein_S14_121279..121429_POSITIVE 282 189 141 140 100 smit:SMT_808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_717897..718047_NEGATIVE 270 201 164 89 57 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 263 60 11 150 98 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 261 170 123 139 68 smit:SMT_1357|3end_endo-beta-N-acetylglucosaminidase_1334450..1334600_NEGATIVE 261 162 121 130 92 smit:SMT_312|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_253926..254076_POSITIVE 257 60 11 126 66 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 253 98 61 50 10 smit:SMT_843|3end_hypothetical_protein_789264..789414_NEGATIVE 251 31 2 47 11 smit:SMT_1621|3end_K09134_hypothetical_protein_1607256..1607406_NEGATIVE 251 64 33 142 116 smit:SMT_602|3end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517964..518114_POSITIVE 245 187 145 121 77 smit:SMT_1014|3end_galactokinase_950645..950795_NEGATIVE 242 115 78 142 101 smit:SMT_801|3end_glycyl-tRNA_synthetase_alpha_chain_709892..710042_NEGATIVE 241 60 14 60 9 smit:SMT_669|3end_ribose-phosphate_pyrophosphokinase_579199..579349_POSITIVE 240 183 142 70 25 smit:SMT_606|3end_cytochrome_c-type_biogenesis_protein_CcdA_520147..520297_POSITIVE 238 90 41 60 10 smit:SMT_628|3end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_534050..534200_POSITIVE 235 200 160 131 86 smit:SMT_1857|3end_hypothetical_protein_1821145..1821295_POSITIVE 234 66 35 142 117 smit:SMT_1555|3end_hypothetical_protein_1540223..1540373_NEGATIVE 233 113 72 69 28 smit:SMT_1261|3end_MutT/NUDIX_family_protein_1227094..1227244_POSITIVE 229 47 2 67 20 smit:SMT_1367|3end_K02237_competence_protein_ComEA_1346872..1347022_NEGATIVE 229 187 142 151 113 smit:SMT_740|3end_50S_ribosomal_protein_L10_643715..643865_NEGATIVE