Origin IGS: tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga .........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 tcgtctctcccatctcttttataccattatatcatttttagacaaaatagacaaaggtacaattttatttcaaaaaccaattcgcaaaccagcccttcctctcaagtaagataagtgacaccacatagacaataaaaaaaccgatgattttccaatcaacggttcttttttgttgtcttaga Mask Tandem Repeat Region ================================================ tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga Find is-nt database================================================ Query_seq: SSA_0848:SSA_0849|SSA_0848:SSA_0849:Pyruvate kinase I, fructose-stimulated, putative:Signal peptidase I, putative:->->:836085..836266 182 tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0848:SSA_0849|SSA_0848:SSA_0849:Pyruvate kinase I, fructose-stimulated, putative:Signal peptidase I, putative:->->:836085..836266 182 tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0848:SSA_0849|SSA_0848:SSA_0849:Pyruvate kinase I, fructose-stimulated, putative:Signal peptidase I, putative:->->:836085..836266 182 tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga Predict ORF larger than 30AA ================================================ tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga 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: 128 End: 157 ...............................................................................................................................TTTGTCTATTTTGTCTAAAAATGATATAAT......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -5.6 Tail_Score: -5.64304 Start: 18 End: 45 Full_Region: acatagacaataaaa aaaccgatgatt ttcc aatcaacggttc ttttttgttgtctta .................aaaccgatgattttccaatcaacggttc......................................................................................................................................... TransTerm Strand: - Conf: 86 HP_score: -7.3 Tail_Score: -4.84921 Start: 21 End: 42 Full_Region: tagacaataaaaaaa ccgatgatt ttcc aatcaacgg ttcttttttgttgtc ....................ccgatgattttccaatcaacgg............................................................................................................................................ Find igs database================================================ Query_seq: SSA_0848:SSA_0849|SSA_0848:SSA_0849:Pyruvate kinase I, fructose-stimulated, putative:Signal peptidase I, putative:->->:836085..836266 182 tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_009009_SSA_0848_SSA_0849|Pyruvate kinase I, fructose-stimulated, putative:Signal peptidase I, putative|POSITIVE:POSITIVE|[836085,836266]|182 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 tctaagacaacaaaaaagaaccgttgattggaaaatcatcggnnnnnnnattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga tctaagacaacaaaaaagaaccgttgattggaaaatcatcggtttttttattgtctatgtggtgtcacttatcttacttgagaggaagggctggtttgcgaattggtttttgaaataaaattgtacctttgtctattttgtctaaaaatgatataatggtataaaagagatgggagagacga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAAGACAACAAAAAAGAACCGUUGAUUGGAAAAUCAUCGGUUUUUUUAUUGUCUAUGUGGUGUCACUUAUCUUACUUGAGAGGAAGGGCUGGUUUGCGAAUUGGUUUUUGAAAUAAAAUUGUACCUUUGUCUAUUUUGUCUAAAAAUGAUAUAAUGGUAUAAAAGAGAUGGGAGAGACGA ....((((((...((((((((((.(((((....))))).)))))))))).)))))).....((.((.((((((((..........((((((..(((....)))..)))))).........(((((((..((((.(((((.....)))))))))....)))))))..)))))))).)).)).. (-52.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUCUCUCCCAUCUCUUUUAUACCAUUAUAUCAUUUUUAGACAAAAUAGACAAAGGUACAAUUUUAUUUCAAAAACCAAUUCGCAAACCAGCCCUUCCUCUCAAGUAAGAUAAGUGACACCACAUAGACAAUAAAAAAACCGAUGAUUUUCCAAUCAACGGUUCUUUUUUGUUGUCUUAGA ..(((.((...((((..(((.((((......(((((((.....))))).))....))))........................((......))..........)))..)))).)).))).......(((((((((((((((((.(((((....))))).))))..))))))))))))).... (-29.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 95 52 227 180 NC_009009:SSA_2030|5end_hypothetical_protein_2036750..2036980_NEGATIVE 290 99 53 178 138 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 280 110 70 230 181 NC_009009:SSA_0523|5end_Aldehyde_dehydrogenase,_putative_521637..521867_POSITIVE 264 99 59 202 167 NC_009009:SSA_2000|5end_hypothetical_protein_1997469..1997699_NEGATIVE 264 99 51 190 138 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 263 107 61 112 65 NC_009009:SSA_2162|5end_hypothetical_protein_2160592..2160822_POSITIVE 260 100 51 200 140 NC_009009:SSA_1061|5end_50S_ribosomal_protein_L21,_putative_1077592..1077822_POSITIVE 258 114 72 134 98 NC_009009:SSA_0954|5end_hypothetical_protein_958024..958254_POSITIVE 258 102 61 188 136 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 256 99 52 221 150 NC_009009:SSA_2206|5end_hypothetical_protein_2206839..2207069_POSITIVE 252 98 52 129 82 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 252 100 59 197 154 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 252 96 57 197 158 NC_009009:SSA_0254|5end_hypothetical_protein_247492..247722_NEGATIVE 250 100 53 84 23 NC_009009:SSA_0605|5end_Methyltransferase_gidB,_putative_593707..593937_NEGATIVE 250 99 63 88 57 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 249 113 77 163 121 NC_009009:SSA_0504|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503009..503239_POSITIVE 249 99 60 55 13 NC_009009:SSA_0493|5end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_492868..493098_POSITIVE 249 93 56 61 19 NC_009009:SSA_0242|5end_hypothetical_protein_234978..235208_POSITIVE 248 91 51 226 190 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 247 100 54 185 136 NC_009009:SSA_2046|5end_Uridine_phosphorylase,_putative_2049721..2049951_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 109 63 85 33 NC_009009:SSA_1226|3end_ParC,_putative_1248783..1248933_NEGATIVE 293 56 11 86 38 NC_009009:SSA_0848|3end_Pyruvate_kinase_I,_fructose-stimulated,_putative_836024..836174_POSITIVE 277 115 79 41 4 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 258 114 72 125 89 NC_009009:SSA_0952|3end_hypothetical_protein_958095..958245_POSITIVE 253 107 67 141 89 NC_009009:SSA_1390|3end_hypothetical_protein_1405633..1405783_NEGATIVE 252 98 52 136 89 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 251 106 61 88 42 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 249 93 56 60 18 NC_009009:SSA_0241|3end_Ribosomal_protein_L11_methyltransferase,_putative_235057..235207_POSITIVE 246 70 21 49 4 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 244 94 52 122 79 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 243 57 11 125 59 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 243 106 77 40 6 NC_009009:SSA_1431|3end_hypothetical_protein_1438047..1438197_NEGATIVE 243 134 95 49 13 NC_009009:SSA_1184|3end_DNA_topoisomerase_I,_putative_1211512..1211662_NEGATIVE 242 98 62 142 108 NC_009009:SSA_0596|3end_hypothetical_protein_587352..587502_POSITIVE 239 84 41 65 13 NC_009009:SSA_2164|3end_Glutamine_amidotransferase,_putative_2160866..2161016_NEGATIVE 234 87 59 31 5 NC_009009:SSA_0813|3end_Thioredoxin_reductase,_putative_794438..794588_NEGATIVE 232 111 77 32 2 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 232 100 51 67 11 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 228 105 61 133 95 NC_009009:SSA_1789|3end_Metal-dependent_phosphohydrolase,_HD_superfamily,_putative_1772365..1772515_NEGATIVE 227 100 51 76 7 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE