Origin IGS: ttctgggaataaggagtaatatatatgaaaaaaatttttattattttatttttgatgttatcaatttttacaataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcttctttaattttcttatctatttcagtaaaaaagttatttaattctttttcagttttaaacggattagcatttattattgtaaaaattgataacatcaaaaataaaataataaaaatttttttcatatatattactccttattcccagaa Mask Tandem Repeat Region ================================================ ttctgggaataaggagtaatatatatgaaaaaaatttttattattttatttttgatgttatcaatttttacaataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa Find is-nt database================================================ Query_seq: FN1513:FN1514|FN1513:FN1514:Phophatidylinositol-4-phosphate 5-kinase:Phophatidylinositol-4-phosphate 5-kinase:->->:17363..17515 153 ttctgggaataaggagtaatatatatgaaaaaaatttttattattttatttttgatgttatcaatttttacaataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1513:FN1514|FN1513:FN1514:Phophatidylinositol-4-phosphate 5-kinase:Phophatidylinositol-4-phosphate 5-kinase:->->:17363..17515 153 ttctgggaataaggagtaatatatatgaaaaaaatttttattattttatttttgatgttatcaatttttacaataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1513:FN1514|FN1513:FN1514:Phophatidylinositol-4-phosphate 5-kinase:Phophatidylinositol-4-phosphate 5-kinase:->->:17363..17515 153 ttctgggaataaggagtaatatatatgaaaaaaatttttattattttatttttgatgttatcaatttttacaataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctgggaataaggagtaatatatatgaaaaaaatttttattattttatttttgatgttatcaatttttacaataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 19 End: 153 .................. M Y M K K I F I I L F L M L S I F T I I N A N P F K T E K E L N N F F T E I D K K I K E E Protein_Len: 47 Strand: - Start: 3 End: 143 .. Q S Y P T I Y I F F I K I I K N K I N D I K V I I F A L G N L V S F S N F L K K V S I S L F M .......... ttctgggaataaggagtaatatatatgaaaaaaatttttattattttatttttgatgttatcaatttttacaataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa 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================================================ ttctgggaataaggagtaatatatatgaaaaaaatttttattattttatttttgatgttatcaatttttacaataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1513:FN1514|FN1513:FN1514:Phophatidylinositol-4-phosphate 5-kinase:Phophatidylinositol-4-phosphate 5-kinase:->->:17363..17515 153 ttctgggaataaggagtaatatatatgaaaaaaatttttattattttatttttgatgttatcaatttttacaataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_003454_FN1513_FN1514|Phophatidylinositol-4-phosphate 5-kinase:Phophatidylinositol-4-phosphate 5-kinase|POSITIVE:POSITIVE|[17363,17515]|153 HSP 1 e-value: 5.0E-40 bit: 165.0 Len: 83 Query Start:71 Query End:153 Subject Strand: POSITIVE Subject Start: 71 Subject End: 153 ......................................................................caataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa ......................................................................caataataaatgctaatccgtttaaaactgaaaaagaattaaataacttttttactgaaatagataagaaaattaaagaagaa HSP 2 e-value: 1.0E-6 bit: 54.0 Len: 27 Query Start:1 Query End:27 Subject Strand: POSITIVE Subject Start: 1 Subject End: 27 ttctgggaataaggagtaatatatatg.............................................................................................................................. ttctgggaataaggagtaatatatatg.............................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGGGAAUAAGGAGUAAUAUAUAUGAAAAAAAUUUUUAUUAUUUUAUUUUUGAUGUUAUCAAUUUUUACAAUAAUAAAUGCUAAUCCGUUUAAAACUGAAAAAGAAUUAAAUAACUUUUUUACUGAAAUAGAUAAGAAAAUUAAAGAAGAA ((((..((...((((((((.(((.((((((.....))))))))).))))))))..(.(((((.(((((........((((((......))))))....((((((((..........))))))))..))))).))))).)...))..))))... (-16.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUCUUUAAUUUUCUUAUCUAUUUCAGUAAAAAAGUUAUUUAAUUCUUUUUCAGUUUUAAACGGAUUAGCAUUUAUUAUUGUAAAAAUUGAUAACAUCAAAAAUAAAAUAAUAAAAAUUUUUUUCAUAUAUAUUACUCCUUAUUCCCAGAA .............((((..........(((((.........(((((((.(((........))).)))))))..(((((((((.......(((((...)))))......))))))))).................)))))..........)))) (-11.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 206 70 22 97 46 NC_003454:FN0307|5end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_942095..942325_POSITIVE 192 69 34 95 63 NC_003454:FN1125|5end_LemA_protein_1769811..1770041_NEGATIVE 189 110 69 132 80 NC_003454:FN0642|5end_hypothetical_protein_1299461..1299691_NEGATIVE 171 102 71 80 53 NC_003454:FN1807|5end_hypothetical_protein_289479..289709_NEGATIVE 170 126 87 49 11 NC_003454:FN0715|5end_hypothetical_protein_1373104..1373334_POSITIVE 165 89 44 172 134 NC_003454:FN1541|5end_Heptaprenyl_diphosphate_synthase_component_II_55215..55445_POSITIVE 160 94 53 141 91 NC_003454:FN1866|5end_Lysine_2,3-aminomutase_358440..358670_NEGATIVE 157 39 1 68 26 NC_003454:FN0561|5end_Proline_synthetase_associated_protein_1214155..1214385_POSITIVE 157 124 81 103 53 NC_003454:FN1900|5end_pfoS/R_388244..388474_POSITIVE 155 63 35 119 85 NC_003454:FN1444|5end_GMP_synthase_[glutamine-hydrolyzing]_2111585..2111815_POSITIVE 155 149 102 231 179 NC_003454:FN1291|5end_hypothetical_protein_1949207..1949437_NEGATIVE 154 89 45 166 120 NC_003454:FN0702|5end_N-acyl-L-amino_acid_amidohydrolase_1361002..1361232_NEGATIVE 154 70 34 136 105 NC_003454:FN2116|5end_Hypothetical_exported_24-amino_acid_repeat_protein_625504..625734_NEGATIVE 154 78 31 173 129 NC_003454:FN1849|5end_Coenzyme_F390_synthetase_337934..338164_POSITIVE 153 95 61 37 3 NC_003454:FN0087|5end_Ethanolamine_utilization_protein_eutN_724626..724856_POSITIVE 152 140 94 208 166 NC_003454:FN0127|5end_Fe-S_oxidoreductase_756312..756542_NEGATIVE 150 65 21 212 164 NC_003454:FN1144|5end_hypothetical_protein_1794152..1794382_NEGATIVE 150 75 35 144 95 NC_003454:FN0263|5end_Peptidyl-prolyl_cis-trans_isomerase_890064..890294_POSITIVE 147 66 26 66 17 NC_003454:FN0778|5end_Methyltransferase_1436087..1436317_NEGATIVE 147 101 81 76 59 NC_003454:FN0163|5end_5-methyltetrahydrofolate--homocysteine_methyltransferase_791318..791548_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 206 70 22 103 52 NC_003454:FN0306|3end_Iron(III)_dicitrate_transport_system_permease_protein_fecD_942181..942331_POSITIVE 192 69 34 86 54 NC_003454:FN1126|3end_Acetyltransferase_1769820..1769970_NEGATIVE 174 120 83 151 117 NC_003454:FN1345|3end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase_1998130..1998280_NEGATIVE 171 102 71 31 4 NC_003454:FN1808|3end_hypothetical_protein_289528..289678_NEGATIVE 167 48 2 93 46 NC_003454:FN1175|3end_hypothetical_protein_1836557..1836707_NEGATIVE 157 39 1 52 10 NC_003454:FN0560|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_1214219..1214369_POSITIVE 154 89 45 100 54 NC_003454:FN0703|3end_N-acyl-L-amino_acid_amidohydrolase_1361068..1361218_NEGATIVE 154 70 34 115 84 NC_003454:FN2117|3end_Hypothetical_exported_24-amino_acid_repeat_protein_625525..625675_NEGATIVE 154 78 31 142 98 NC_003454:FN1848|3end_Metal_dependent_hydrolase_337983..338133_POSITIVE 153 95 61 35 1 NC_003454:FN0086|3end_hypothetical_protein_724704..724854_POSITIVE 151 46 1 142 111 NC_003454:FN0171|3end_Hypothetical_cytosolic_protein_796921..797071_POSITIVE 150 65 21 112 64 NC_003454:FN1145|3end_Oligoendopeptidase_F_1794252..1794402_NEGATIVE 147 66 26 57 8 NC_003454:FN0779|3end_Putative_GTPase_(G3E_family)_1436096..1436246_NEGATIVE 147 84 57 124 94 NC_003454:FN0777|3end_GTP-binding_protein_LepA_1433018..1433168_NEGATIVE 147 101 81 22 5 NC_003454:FN0162|3end_Na+_driven_multidrug_efflux_pump_791344..791494_POSITIVE 146 79 34 88 40 NC_003454:FN0075|3end_Ethanolamine_utilization_protein_eutP_714216..714366_POSITIVE 145 93 56 40 12 NC_003454:FN1440|3end_1-phosphofructokinase_2108262..2108412_POSITIVE 145 24 3 91 71 NC_003454:FN1307|3end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_1964056..1964206_POSITIVE 139 115 73 70 28 NC_003454:FN0976|3end_hypothetical_protein_1628146..1628296_NEGATIVE 139 69 31 116 81 NC_003454:FN1846|3end_hypothetical_protein_336225..336375_POSITIVE