Origin IGS: tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat .........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 atagctctcctatcttagttgccaactttggaattaaaatttgatttttaatattttagcataaaatagcagaaaacaaaagtgaggttttttacatgagaaagcaaaagctagtgcctttattcttcctattttttgaaggaattattatcgttggaggctagctctaagaagttatactcaatgaaaaaagcctgagatactcatctcaagctctattttctaaa Mask Tandem Repeat Region ================================================ tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat Find is-nt database================================================ Query_seq: SMT_1307:SMT_1308|SMT_1307:SMT_1308:glycerol uptake facilitator protein:hypothetical protein:->->:1272509..1272735 227 tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1307:SMT_1308|SMT_1307:SMT_1308:glycerol uptake facilitator protein:hypothetical protein:->->:1272509..1272735 227 tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1307:SMT_1308|SMT_1307:SMT_1308:glycerol uptake facilitator protein:hypothetical protein:->->:1272509..1272735 227 tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 96 End: 191 ............................................................................................... M G R I K A L A F A F S C K K P H F C F L L F Y A K I L K I K F .................................... Protein_Len: 32 Strand: - Start: 67 End: 162 .................................................................. G G V I I I G E F F L F F L P V L K Q K R M Y F V E S K N E A M ................................................................. tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat 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================================================ tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1307:SMT_1308|SMT_1307:SMT_1308:glycerol uptake facilitator protein:hypothetical protein:->->:1272509..1272735 227 tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat Intra-Species Hit: Count: 1 Min: 1 Max: 227 Len: 227 Subject: smit_SMT_1307_SMT_1308|glycerol uptake facilitator protein:hypothetical protein|POSITIVE:POSITIVE|[1272509,1272735]|227 HSP 1 e-value: 1.0E-126 bit: 450.0 Len: 227 Query Start:1 Query End:227 Subject Strand: POSITIVE Subject Start: 1 Subject End: 227 tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat tttagaaaatagagcttgagatgagtatctcaggcttttttcattgagtataacttcttagagctagcctccaacgataataattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaagataggagagctat Inter-species Hit: Count: 1 Min: 51 Max: 213 Len: 163 Subject: NC_008533_SPD_2007_SPD_2009|transporter, major facilitator family protein:hypothetical protein|NEGATIVE:POSITIVE|[1983163,1986005]|2843 HSP 1 e-value: 8.0E-43 bit: 174.0 Len: 163 Query Start:51 Query End:213 Subject Strand: NEGATIVE Subject Start: 15 Subject End: 179 ..................................................taacttcttagagctagcctccaacgataat---aattccttcaaaaaataggaagaataaaggcactagcttttgctttctcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaattttaattccaaagttggcaactaa.............. ..................................................taacttcttagtactagccaacaacgataatcataattcctcctaaaattaggaataataaaggcaatagtttttgttttttcatgtaaaaaacctcacttttgttttctgctattttatgctaaaatattaaaaatcaaa-tttaattccaaagtttgtaactaa.............. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUCUUAGAGCUAGCCUCCAACGAUAAUAAUUCCUUCAAAAAAUAGGAAGAAUAAAGGCACUAGCUUUUGCUUUCUCAUGUAAAAAACCUCACUUUUGUUUUCUGCUAUUUUAUGCUAAAAUAUUAAAAAUCAAAUUUUAAUUCCAAAGUUGGCAACUAA ............((((((.....................((.(((((((.(((((((((((.......((((((........)))))).......)))))))))).).))))))).)).......(((((((......)))))))......))))))...... (-23.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGUUGCCAACUUUGGAAUUAAAAUUUGAUUUUUAAUAUUUUAGCAUAAAAUAGCAGAAAACAAAAGUGAGGUUUUUUACAUGAGAAAGCAAAAGCUAGUGCCUUUAUUCUUCCUAUUUUUUGAAGGAAUUAUUAUCGUUGGAGGCUAGCUCUAAGAAGUUA (((((..(((((...(((((((.....)))))))(((((.(((..((.(((((((.((((..((..(((...(((((((.....)))))))....)))..))......))))..))))))).))...))).)))))..)))))..)))))............. (-28.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 42 2 127 84 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 287 86 58 214 184 smit:SMT_1826|5end_ATP_synthase_beta_chain_1797408..1797638_POSITIVE 287 86 58 214 184 smit:SMT_586|5end_ATP_synthase_F1,_beta_subunit_502533..502763_POSITIVE 275 110 61 60 22 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 275 110 61 60 22 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 272 103 61 121 79 smit:SMT_1965|5end_hypothetical_protein_1897044..1897274_POSITIVE 272 103 61 121 79 smit:SMT_74|5end_hypothetical_protein_2197..2427_NEGATIVE 251 40 2 79 29 smit:SMT_676|5end_DNA_helicase_II_585266..585496_NEGATIVE 249 110 67 86 48 smit:SMT_1976|5end_immunoglobulin_A1_protease_1906950..1907180_POSITIVE 245 110 61 223 173 smit:SMT_1680|5end_hypothetical_protein_1663494..1663724_POSITIVE 243 39 2 117 81 smit:SMT_1566|5end_K03475_PTS_system,_unknown_pentitol_phosphotransferase_enzyme_IIC_component_1557918..1558148_POSITIVE 243 120 72 147 91 smit:SMT_1214|5end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1173422..1173652_NEGATIVE 240 21 4 46 27 smit:SMT_1555|5end_hypothetical_protein_1541014..1541244_NEGATIVE 237 109 61 124 66 smit:SMT_2152|5end_cell_division_protein_2025649..2025879_POSITIVE 237 74 35 181 144 smit:SMT_1348|5end_exoribonuclease_II_1327502..1327732_NEGATIVE 237 39 3 122 82 smit:SMT_1263|5end_hypothetical_protein_1228104..1228334_POSITIVE 236 76 34 154 99 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 234 110 61 121 69 smit:SMT_359|5end_transcription_termination-antitermination_factor_294470..294700_POSITIVE 221 57 11 197 152 smit:SMT_1623|5end_K03498_trk_system_potassium_uptake_protein_TrkH_1609596..1609826_POSITIVE 221 79 32 48 5 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 42 2 96 53 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 287 86 58 128 98 smit:SMT_1825|3end_ATP_synthase_F1,_gamma_subunit_1797402..1797552_POSITIVE 287 86 58 128 98 smit:SMT_585|3end_ATP_synthase_gamma_chain_502527..502677_POSITIVE 275 110 61 63 25 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 243 39 2 104 68 smit:SMT_1565|3end_PTS_system,_IIB_component,_putative_1557985..1558135_POSITIVE 243 120 72 150 94 smit:SMT_1215|3end_aromatic_amino_acid_aminotransferase_1173419..1173569_NEGATIVE 237 74 35 79 42 smit:SMT_1349|3end_K03075_preprotein_translocase_SecG_subunit_1327604..1327754_NEGATIVE 237 39 3 120 80 smit:SMT_1262|3end_ribosomal_protein_L11_methyltransferase_1228182..1228332_POSITIVE 234 110 61 77 25 smit:SMT_358|3end_hypothetical_protein_294506..294656_POSITIVE 227 40 5 42 4 smit:SMT_677|3end_DNA_topoisomerase_I_585303..585453_NEGATIVE 221 79 32 61 18 smit:SMT_1455|3end_deoxyribose-phosphate_aldolase_1437873..1438023_NEGATIVE 217 28 2 31 8 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 217 82 48 91 50 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 216 30 7 34 5 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 212 110 62 134 80 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 212 40 4 138 96 smit:SMT_567|3end_conserved_hypothetical_protein_485752..485902_POSITIVE 211 76 35 92 46 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 211 75 39 102 63 smit:SMT_662|3end_A/G-specific_adenine_glycosylase_572652..572802_NEGATIVE 210 107 64 106 61 smit:SMT_396|3end_putative_nicotinate_phosphoribosyltransferase_326602..326752_POSITIVE 208 108 64 137 86 smit:SMT_790|3end_hypothetical_protein_701093..701243_NEGATIVE