Origin IGS: tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaacaaagagcagtcccagggattgcttttttgtgttggttttaagtggcatcttgatttttaaagtggtataataaatgcaatttgatgagttagaaagaacaaa Mask Tandem Repeat Region ================================================ tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt Find is-nt database================================================ Query_seq: SSA_2087:SSA_2088|SSA_2087:SSA_2088:Conserved uncharacterized protein:Carbohydrate isomerase, AraD/FucA family, putative:<-<-:2092748..2092855 108 tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2087:SSA_2088|SSA_2087:SSA_2088:Conserved uncharacterized protein:Carbohydrate isomerase, AraD/FucA family, putative:<-<-:2092748..2092855 108 tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2087:SSA_2088|SSA_2087:SSA_2088:Conserved uncharacterized protein:Carbohydrate isomerase, AraD/FucA family, putative:<-<-:2092748..2092855 108 tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt Predict ORF larger than 30AA ================================================ tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt 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: 82 Start: 7 End: 36 ......CTTTCTAACTCATCAAATTGCATTTATTAT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2087:SSA_2088|SSA_2087:SSA_2088:Conserved uncharacterized protein:Carbohydrate isomerase, AraD/FucA family, putative:<-<-:2092748..2092855 108 tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_009009_SSA_2087_SSA_2088|Conserved uncharacterized protein:Carbohydrate isomerase, AraD/FucA family, putative|NEGATIVE:NEGATIVE|[2092748,2092855]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt tttgttctttctaactcatcaaattgcatttattataccactttaaaaatcaagatgccacttaaaaccaacacaaaaaagcaatccctgggactgctctttgttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUUCUUUCUAACUCAUCAAAUUGCAUUUAUUAUACCACUUUAAAAAUCAAGAUGCCACUUAAAACCAACACAAAAAAGCAAUCCCUGGGACUGCUCUUUGUUUUU .........................((((((.....................))))))..............(((((..((((.(((...))).)))).))))).... (-10.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACAAAGAGCAGUCCCAGGGAUUGCUUUUUUGUGUUGGUUUUAAGUGGCAUCUUGAUUUUUAAAGUGGUAUAAUAAAUGCAAUUUGAUGAGUUAGAAAGAACAAA ......((((((((((((...))))))))))))..((((..((((((....((((..........((((.((((.....)))).))))))))..))))))..)))).. (-21.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 913 100 51 191 142 NC_009009:SSA_2087|5end_Conserved_uncharacterized_protein_2092657..2092887_NEGATIVE 250 99 51 105 49 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 246 100 51 76 22 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 245 100 54 62 1 NC_009009:SSA_2258|5end_hypothetical_protein_2254699..2254929_NEGATIVE 244 99 56 66 25 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 232 98 60 148 106 NC_009009:SSA_1525|5end_Lyzozyme_M1_(1,4-beta-N-acetylmuramidase),_putative_1532746..1532976_POSITIVE 232 92 51 45 8 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 228 98 53 230 178 NC_009009:SSA_0409|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_405605..405835_NEGATIVE 225 100 69 76 47 NC_009009:SSA_1408|5end_hypothetical_protein_1421005..1421235_NEGATIVE 216 58 15 50 12 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 215 98 52 84 34 NC_009009:SSA_1199|5end_Phosphinothricin_acetyltransferase,_putative_1223958..1224188_NEGATIVE 213 93 52 73 33 NC_009009:SSA_2153|5end_ABC-type_transporter_(uncharacterized),_permease_component,_putative_2154664..2154894_NEGATIVE 212 99 86 19 4 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 212 99 81 228 207 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 211 97 57 167 122 NC_009009:SSA_1352|5end_hypothetical_protein_1367941..1368171_NEGATIVE 210 99 53 50 6 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 209 98 51 65 24 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 207 98 51 222 176 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 206 100 65 226 182 NC_009009:SSA_1291|5end_hypothetical_protein_1311102..1311332_NEGATIVE 204 98 59 197 151 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 99 51 68 12 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 246 100 51 62 8 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 244 99 56 47 6 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 228 98 53 85 33 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 224 93 55 35 1 NC_009009:SSA_0066|3end_hypothetical_protein_68095..68245_POSITIVE 217 93 56 66 29 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 217 98 73 102 76 NC_009009:SSA_0274|3end_hypothetical_protein_268580..268730_NEGATIVE 215 98 52 121 71 NC_009009:SSA_1200|3end_Formate--tetrahydrofolate_ligase,_putative_1223921..1224071_NEGATIVE 211 97 57 134 89 NC_009009:SSA_1353|3end_hypothetical_protein_1367974..1368124_NEGATIVE 203 100 56 134 79 NC_009009:SSA_1978|3end_Dihydroxyacetone_kinase_family_protein_(Dak2_domain),_putative_1972269..1972419_NEGATIVE 202 93 52 61 10 NC_009009:SSA_0385|3end_ABC_transporter,_glycine-betaine/proline_permease_protein,_putative_378526..378676_NEGATIVE 202 100 58 119 77 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 200 100 53 91 31 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 199 100 60 91 45 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 197 98 55 71 19 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 195 99 78 120 93 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 195 96 52 58 13 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 193 96 57 57 18 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 191 99 84 69 53 NC_009009:SSA_0469|3end_Precorrin-6B_methylase_2,putative_472959..473109_POSITIVE 187 96 51 146 103 NC_009009:SSA_1094|3end_GTP-binding_protein,_putative_1112243..1112393_POSITIVE