Origin IGS: cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtccgcatccagctccaattcttgagcagcctgaataaaatcatggaataattgnnnnnttaattaattaannnnncaccctgagtcccaaacctccttcatctaag Mask Tandem Repeat Region ================================================ cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac Find is-nt database================================================ Query_seq: SMT_1472:SMT_1473|SMT_1472:SMT_1473:hypothetical protein, coenzyme PQQ synthesis homologue:hypothetical protein:<-->:1454353..1454459 107 cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1472:SMT_1473|SMT_1472:SMT_1473:hypothetical protein, coenzyme PQQ synthesis homologue:hypothetical protein:<-->:1454353..1454459 107 cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1472:SMT_1473|SMT_1472:SMT_1473:hypothetical protein, coenzyme PQQ synthesis homologue:hypothetical protein:<-->:1454353..1454459 107 cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac Predict ORF larger than 30AA ================================================ cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac 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================================================ cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1472:SMT_1473|SMT_1472:SMT_1473:hypothetical protein, coenzyme PQQ synthesis homologue:hypothetical protein:<-->:1454353..1454459 107 cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: smit_SMT_1472_SMT_1473|hypothetical protein, coenzyme PQQ synthesis homologue:hypothetical protein|NEGATIVE:POSITIVE|[1454353,1454459]|107 HSP 1 e-value: 1.0E-36 bit: 153.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac cttagatgaaggaggtttgggactcagggtgnnnnnttaattaattaannnnncaattattccatgattttattcaggctgctcaagaattggagctggatgcggac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAGAUGAAGGAGGUUUGGGACUCAGGGUGNNNNNUUAAUUAAUUAANNNNNCAAUUAUUCCAUGAUUUUAUUCAGGCUGCUCAAGAAUUGGAGCUGGAUGCGGAC ......((((.(((((((((((.......((.....((((....)))).....))....))))).)))))).)))).((.((((........)))).....)).... (-13.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCCGCAUCCAGCUCCAAUUCUUGAGCAGCCUGAAUAAAAUCAUGGAAUAAUUGNNNNNUUAAUUAAUUAANNNNNCACCCUGAGUCCCAAACCUCCUUCAUCUAAG .(((.......((((........))))....(((......))).))).((((((......))))))................(((........)))........... ( -8.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 804 100 54 191 145 smit:SMT_1472|5end_hypothetical_protein,_coenzyme_PQQ_synthesis_homologue_1454262..1454492_NEGATIVE 256 31 1 100 63 smit:SMT_1743|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1725156..1725386_NEGATIVE 253 99 65 71 38 smit:SMT_1418|5end_lysine_decarboxylase_1403147..1403377_NEGATIVE 244 100 73 205 181 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 240 97 74 228 203 smit:SMT_1288|5end_replicative_DNA_helicase_1250854..1251084_POSITIVE 239 95 75 171 146 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 231 100 61 221 190 smit:SMT_2148|5end_hypothetical_protein_2023635..2023865_NEGATIVE 227 96 61 70 24 smit:SMT_415|5end_hypothetical_protein_358785..359015_POSITIVE 221 100 75 189 156 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 219 99 62 211 175 smit:SMT_466|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_403645..403875_POSITIVE 215 31 2 225 199 smit:SMT_1770|5end_hypothetical_protein_1746505..1746735_NEGATIVE 213 100 60 143 104 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 212 30 8 182 159 smit:SMT_1397|5end_mutator_MutT_protein_1372727..1372957_POSITIVE 211 22 4 22 6 smit:SMT_2097|5end_type_I_restriction_enzyme_M_protein_1991272..1991502_NEGATIVE 210 29 5 120 95 smit:SMT_472|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_409494..409724_NEGATIVE 210 29 5 120 95 smit:SMT_469|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_405812..406042_NEGATIVE 209 100 54 190 134 smit:SMT_556|5end_putative_aminotransferase_473544..473774_POSITIVE 208 28 4 215 193 smit:SMT_413|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_356677..356907_POSITIVE 208 98 54 223 173 smit:SMT_100|5end_hypoxanthine-guanine_phosphoribosyltransferase_31471..31701_POSITIVE 207 97 54 170 103 smit:SMT_1747|5end_anthranilate_synthase_component_I_1726279..1726509_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 500 28 1 148 121 smit:SMT_1007|3end_radical_SAM_domain_protein_947549..947699_POSITIVE 256 31 1 60 23 smit:SMT_1744|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1725196..1725346_NEGATIVE 231 96 55 126 86 smit:SMT_763|3end_alpha-amylase_669280..669430_POSITIVE 230 99 75 46 20 smit:SMT_1489|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1470714..1470864_POSITIVE 227 30 11 65 40 smit:SMT_1015|3end_galactose_operon_repressor_953019..953169_POSITIVE 227 96 61 77 31 smit:SMT_414|3end_K03665_GTP-binding_protein_HflX_358872..359022_POSITIVE 218 98 70 122 95 smit:SMT_1279|3end_translation_elongation_factor_Ts_1243451..1243601_POSITIVE 213 99 60 144 103 smit:SMT_1370|3end_K06217_phosphate_starvation-inducible_protein_PhoH_and_related_proteins_1349499..1349649_NEGATIVE 213 100 60 146 107 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 211 100 64 56 24 smit:SMT_444|3end_thiamine-phosphate_pyrophosphorylase_384048..384198_POSITIVE 206 99 60 142 113 smit:SMT_1376|3end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1354675..1354825_NEGATIVE 205 94 56 52 14 smit:SMT_719|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_625006..625156_NEGATIVE 201 98 60 123 86 smit:SMT_336|3end_hypothetical_protein_275622..275772_POSITIVE 200 99 60 144 106 smit:SMT_1856|3end_polypeptide_deformylase_1820999..1821149_POSITIVE 200 96 65 62 14 smit:SMT_1694|3end_GTPase_1677632..1677782_POSITIVE 200 99 60 144 106 smit:SMT_835|3end_polypeptide_deformylase_777124..777274_NEGATIVE 197 30 4 140 116 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 197 26 1 69 43 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 194 30 3 66 41 smit:SMT_1805|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1781241..1781391_POSITIVE 194 30 3 66 41 smit:SMT_1634|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621438..1621588_POSITIVE