Origin IGS: tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatccttgaattggtggatttttcaagcttgaaatcataaaatcgaacccaatttaattaatcagttttttctataatattcgctttttctataataaaaggacatttga Mask Tandem Repeat Region ================================================ tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa Find is-nt database================================================ Query_seq: AA01603:AA01604|AA01603:AA01604:oligopeptidase A:conserved hypothetical protein:->->:1085075..1085185 111 tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01603:AA01604|AA01603:AA01604:oligopeptidase A:conserved hypothetical protein:->->:1085075..1085185 111 tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01603:AA01604|AA01603:AA01604:oligopeptidase A:conserved hypothetical protein:->->:1085075..1085185 111 tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa Predict ORF larger than 30AA ================================================ tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa 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: 15 End: 44 ..............TTTTTCTATAATATTCGCTTTTTCTATAAT................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01603:AA01604|AA01603:AA01604:oligopeptidase A:conserved hypothetical protein:->->:1085075..1085185 111 tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: aact_AA01603_AA01604|oligopeptidase A:conserved hypothetical protein|POSITIVE:POSITIVE|[1085075,1085185]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa tcaaatgtccttttattatagaaaaagcgaatattatagaaaaaactgattaattaaattgggttcgattttatgatttcaagcttgaaaaatccaccaattcaaggataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAUGUCCUUUUAUUAUAGAAAAAGCGAAUAUUAUAGAAAAAACUGAUUAAUUAAAUUGGGUUCGAUUUUAUGAUUUCAAGCUUGAAAAAUCCACCAAUUCAAGGAUAA .....(((((((..(((...((..((((....(((((((((....(..(((.....)))..)......))))))))).....))))......))....)))..))))))). (-16.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUCCUUGAAUUGGUGGAUUUUUCAAGCUUGAAAUCAUAAAAUCGAACCCAAUUUAAUUAAUCAGUUUUUUCUAUAAUAUUCGCUUUUUCUAUAAUAAAAGGACAUUUGA ......((((((((((.(((((((((....)))......)))))).)..))))))))).......(((((((.(((.(((...........))).))))))))))...... (-11.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 99 51 146 82 aact:AA00199|5end_hypothetical_protein_138575..138805_POSITIVE 211 97 58 71 14 aact:AA00523|5end_conserved_hypothetical_protein_358472..358702_POSITIVE 209 97 60 214 161 aact:AA01450|5end_hypothetical_protein_971860..972090_POSITIVE 197 108 63 231 185 aact:AA00290|5end_conserved_hypothetical_protein_201272..201502_POSITIVE 196 69 23 110 72 aact:AA00226|5end_hypothetical_protein_156276..156506_POSITIVE 191 100 56 158 120 aact:AA02233|5end_asparaginyl-tRNA_synthetase_1519877..1520107_POSITIVE 191 98 61 36 4 aact:AA00323|5end_conserved_hypothetical_protein_(possible_SAM-dependent_methyltransferase)_219387..219617_POSITIVE 189 109 62 174 120 aact:AA02004|5end_homoserine_O-acetyltransferase_1361937..1362167_POSITIVE 188 98 61 192 146 aact:AA02291|5end_formyltetrahydrofolate_deformylase_1562046..1562276_POSITIVE 187 88 59 224 190 aact:AA02917|5end_cystathionine_gamma-synthase_2042094..2042324_POSITIVE 187 109 81 210 180 aact:AA01871|5end_conserved_hypothetical_protein_1258223..1258453_POSITIVE 183 105 61 129 80 aact:AA00037|5end_conserved_hypothetical_protein_29170..29400_POSITIVE 181 87 46 49 3 aact:AA00003|5end_DNA_replication_and_repair_protein_2337..2567_POSITIVE 178 98 60 145 100 aact:AA01737|5end_exoribonuclease_II_1172647..1172877_POSITIVE 176 100 59 162 125 aact:AA01115|5end_carboxylesterase_766545..766775_POSITIVE 176 100 56 112 77 aact:AA00890|5end_conserved_hypothetical_protein_617075..617305_POSITIVE 173 110 70 195 156 aact:AA02737|5end_conserved_hypothetical_protein_1918666..1918896_POSITIVE 173 99 51 219 169 aact:AA01561|5end_conserved_hypothetical_protein_1046505..1046735_POSITIVE 172 110 61 204 151 aact:AA00747|5end_UTP--hexose-1-phosphate_uridylyltransferase_/_UDPglucose-hexose-1-phosphate_uridylyltransferas_512384..512614_POSITIVE 171 85 53 178 147 aact:AA01808|5end_electron_transport_complex_protein_1217287..1217517_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 99 51 134 70 aact:AA00198|3end_conserved_hypothetical_protein_(Cytosine_deaminase-related_enzyme)_138643..138793_POSITIVE 205 107 61 119 69 aact:AA00135|3end_S-adenosylmethionine:_2-demethylmenaquinone_methyltransferase_(menaquinone_biosynthesis_protein)_96880..97030_POSITIVE 196 87 57 151 117 aact:AA02462|3end_thiol_peroxidase_(scavengase)_1702673..1702823_POSITIVE 188 98 61 54 8 aact:AA02290|3end_cell_division_protein_J;_ribosomal_RNA_large_subunit_methyltransferase_J_1561988..1562138_POSITIVE 184 107 61 119 78 aact:AA02294|3end_conserved_hypothetical_protein_1565367..1565517_POSITIVE 183 105 61 133 84 aact:AA00036|3end_transposase_29254..29404_POSITIVE 178 98 60 132 87 aact:AA01735|3end_hypothetical_protein_1172714..1172864_POSITIVE 176 100 59 45 8 aact:AA01114|3end_alcohol_dehydrogenase,_class_III;_glutathione-dependent_formaldehyde_dehydrogenase_766508..766658_POSITIVE 176 100 56 67 32 aact:AA00889|3end_conserved_hypothetical_protein_617110..617260_POSITIVE 173 99 51 139 89 aact:AA01559|3end_RecA_regulatory_protein,_RecX_1046505..1046655_POSITIVE 172 110 61 134 81 aact:AA00745|3end_galactokinase_512394..512544_POSITIVE 169 107 72 33 3 aact:AA02837|3end_conserved_hypothetical_protein_1992977..1993127_POSITIVE 169 102 77 34 1 aact:AA01603|3end_oligopeptidase_A_1085014..1085164_POSITIVE 169 108 95 83 70 aact:AA01544|3end_conserved_hypothetical_protein_1035433..1035583_POSITIVE 169 95 61 144 104 aact:AA00849|3end_MraZ_cell_division_protein_586786..586936_POSITIVE 169 104 61 146 108 aact:AA00575|3end_shikimate_5-dehydrogenase_394093..394243_POSITIVE 167 108 67 43 6 aact:AA01357|3end_5-formyltetrahydrofolate_cyclo-ligase-family_protein_919785..919935_POSITIVE 166 98 54 81 21 aact:AA00212|3end_ribokinase_147047..147197_POSITIVE 165 70 27 79 29 aact:AA01324|3end_50S_ribosomal_protein_L33_894742..894892_POSITIVE 164 100 60 43 3 aact:AA01945|3end_selenophosphate_synthase_1316022..1316172_POSITIVE