Origin IGS: aatgttaaccttttttattttttgacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta .........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 tagatggattctcctttaaattttccgaggtttcccctcgtttatctattctattttacacaatttttcacaaaaaagctagtcaaaaccaaaaaggaaccgactgtttggcagtgggattgctttaaacaaatataagcaaatatgtgaaaagaaatttccatttcactcttgctaatctccttgctttttgttagaatgatgtcaaaaaataaaaaaggttaacatt Mask Tandem Repeat Region ================================================ aatgttaaccttttttattttttgacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta Find is-nt database================================================ Query_seq: SMT_1555:SMT_1556|SMT_1555:SMT_1556:hypothetical protein:phosphoglycerate mutase:<-->:1541105..1541333 229 aatgttaaccttttttattttttgacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1555:SMT_1556|SMT_1555:SMT_1556:hypothetical protein:phosphoglycerate mutase:<-->:1541105..1541333 229 aatgttaaccttttttattttttgacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1555:SMT_1556|SMT_1555:SMT_1556:hypothetical protein:phosphoglycerate mutase:<-->:1541105..1541333 229 aatgttaaccttttttattttttgacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgttaaccttttttattttttgacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 27 End: 176 .......................... M I L T K S K E I S K S E M E I S F H I F A Y I C L K Q S H C Q T V G S F L V L T S F F V K N C V K ..................................................... Protein_Len: 44 Strand: - Start: 95 End: 226 .............................................................................................. I Q K F C D W Q W V T P E K K T K V L K K T F F Q T F Y F L Y V L P F R P F N L P S D M ... aatgttaaccttttttattttttgacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta 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: 87 Start: 30 End: 59 .............................CTTGCTAATCTCCTTGCTTTTTGTTAGAAT.......................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 85 Start: 106 End: 122 .........................................................................................................TTGGCAGTGGGATTGCT........................................................................................................... aatgttaaccttttttattttttgacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1555:SMT_1556|SMT_1555:SMT_1556:hypothetical protein:phosphoglycerate mutase:<-->:1541105..1541333 229 aatgttaaccttttttattttttgacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta Intra-Species Hit: Count: 1 Min: 24 Max: 229 Len: 206 Subject: smit_SMT_1555_SMT_1556|hypothetical protein:phosphoglycerate mutase|NEGATIVE:POSITIVE|[1541105,1541333]|229 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 206 Query Start:24 Query End:229 Subject Strand: POSITIVE Subject Start: 24 Subject End: 229 .......................gacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta .......................gacatcattctaacaaaaagcaaggagattagcaagagtgaaatggaaatttcttttcacatatttgcttatatttgtttaaagcaatcccactgccaaacagtcggttcctttttggttttgactagcttttttgtgaaaaattgtgtaaaatagaatagataaacgaggggaaacctcggaaaatttaaaggagaatccatcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAUCAUUCUAACAAAAAGCAAGGAGAUUAGCAAGAGUGAAAUGGAAAUUUCUUUUCACAUAUUUGCUUAUAUUUGUUUAAAGCAAUCCCACUGCCAAACAGUCGGUUCCUUUUUGGUUUUGACUAGCUUUUUUGUGAAAAAUUGUGUAAAAUAGAAUAGAUAAACGAGGGGAAACCUCGGAAAAUUUAAAGGAGAAUCCAUCUA .((((.(((...(((((((((..((((...((((((.((((((.(((....)))))))))...)))))).....((((.....)))).....)).))....((((((..((.....))..)))))).)).)))))))....))).))))....((((.(((((...(((((.....)))))....)))))..((.....)).)))) (-45.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUGGAUUCUCCUUUAAAUUUUCCGAGGUUUCCCCUCGUUUAUCUAUUCUAUUUUACACAAUUUUUCACAAAAAAGCUAGUCAAAACCAAAAAGGAACCGACUGUUUGGCAGUGGGAUUGCUUUAAACAAAUAUAAGCAAAUAUGUGAAAAGAAAUUUCCAUUUCACUCUUGCUAAUCUCCUUGCUUUUUGUUAGAAUGAUGUC (((((((.....))...........(((((.....)))))...))))).........(((..(((((..(((((((.((.((..........((((.((((.((((.....)))).)).)).))))...........(((((....((((((.(.......).))))))..)))))......)).))))))))).)))))..))). (-40.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 825 110 61 224 175 smit:SMT_1555|5end_hypothetical_protein_1541014..1541244_NEGATIVE 327 141 103 132 94 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 290 46 1 190 149 smit:SMT_1088|5end_hypothetical_protein_1024346..1024576_NEGATIVE 284 149 101 166 114 smit:SMT_2022|5end_hypothetical_protein_1938257..1938487_POSITIVE 284 200 154 227 173 smit:SMT_978|5end_hypothetical_protein_926607..926837_NEGATIVE 283 130 83 86 41 smit:SMT_1067|5end_alanine_racemase_1005769..1005999_POSITIVE 277 112 84 225 199 smit:SMT_1888|5end_K02026_multiple_sugar_transport_system_permease_protein_1842088..1842318_POSITIVE 274 130 83 126 66 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 263 130 86 186 139 smit:SMT_362|5end_K02519_translation_initiation_factor_IF-2_296230..296460_POSITIVE 260 129 81 219 167 smit:SMT_1591|5end_DNA-entry_nuclease_1578873..1579103_POSITIVE 260 124 88 225 178 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 259 130 82 85 33 smit:SMT_1023|5end_hypothetical_protein_958884..959114_NEGATIVE 259 130 88 205 161 smit:SMT_624|5end_K07584_hypothetical_protein_529870..530100_POSITIVE 257 122 88 119 77 smit:SMT_227|5end_hypothetical_protein_164039..164269_POSITIVE 257 122 88 119 77 smit:SMT_224|5end_hypothetical_protein_158470..158700_POSITIVE 256 128 84 66 20 smit:SMT_1422|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1407467..1407697_NEGATIVE 256 128 84 191 145 smit:SMT_1421|5end_K02003_1407342..1407572_NEGATIVE 255 139 93 88 35 smit:SMT_2034|5end_hydrolase,_haloacid_dehalogenase-like_family_1946671..1946901_POSITIVE 255 130 81 128 62 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 255 130 81 128 62 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 105 61 120 72 smit:SMT_1628|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1616610..1616760_NEGATIVE 327 141 103 145 107 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 284 149 101 123 71 smit:SMT_2021|3end_K06201_copper_homeostasis_protein_1938294..1938444_POSITIVE 283 130 83 96 51 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE 274 130 83 139 79 smit:SMT_1455|3end_deoxyribose-phosphate_aldolase_1437873..1438023_NEGATIVE 261 138 93 72 20 smit:SMT_2046|3end_choline_binding_protein_C_1957280..1957430_NEGATIVE 259 130 88 67 23 smit:SMT_623|3end_50S_ribosomal_protein_L21_529812..529962_POSITIVE 255 139 93 76 23 smit:SMT_2033|3end_hydrolase,_haloacid_dehalogenase-like_family_1946739..1946889_POSITIVE 253 128 82 108 60 smit:SMT_1362|3end_chaperone_protein_hscC_1341414..1341564_NEGATIVE 253 129 84 44 7 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 251 148 101 52 1 smit:SMT_1215|3end_aromatic_amino_acid_aminotransferase_1173419..1173569_NEGATIVE 249 129 87 135 93 smit:SMT_1404|3end_lipoate-protein_ligase_A_1382036..1382186_POSITIVE 249 137 101 59 22 smit:SMT_1243|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1204469..1204619_POSITIVE 247 138 92 98 43 smit:SMT_929|3end_hypothetical_protein_883202..883352_NEGATIVE 245 130 82 71 23 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 245 125 82 80 31 smit:SMT_785|3end_hypothetical_protein_696307..696457_NEGATIVE 244 133 96 63 10 smit:SMT_801|3end_glycyl-tRNA_synthetase_alpha_chain_709892..710042_NEGATIVE 239 130 83 149 97 smit:SMT_1379|3end_thymidylate_kinase_1356800..1356950_NEGATIVE 235 130 83 86 28 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE 235 128 83 59 17 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE