Origin IGS: taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaattccctccaaaaaatttaaaataatagagtttattctataatattttttttaaattgtctagtgaaaagaaaaaaattggattataagttataacccaatttcatta Mask Tandem Repeat Region ================================================ taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa Find is-nt database================================================ Query_seq: FN0161:FN0162|FN0161:FN0162:RNA-directed DNA polymerase:Na+ driven multidrug efflux pump:->->:789953..790063 111 taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0161:FN0162|FN0161:FN0162:RNA-directed DNA polymerase:Na+ driven multidrug efflux pump:->->:789953..790063 111 taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0161:FN0162|FN0161:FN0162:RNA-directed DNA polymerase:Na+ driven multidrug efflux pump:->->:789953..790063 111 taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa Predict ORF larger than 30AA ================================================ taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa 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: 46 End: 75 .............................................CTAGACAATTTAAAAAAAATATTATAGAAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0161:FN0162|FN0161:FN0162:RNA-directed DNA polymerase:Na+ driven multidrug efflux pump:->->:789953..790063 111 taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_003454_FN0161_FN0162|RNA-directed DNA polymerase:Na+ driven multidrug efflux pump|POSITIVE:POSITIVE|[789953,790063]|111 HSP 1 e-value: 5.0E-30 bit: 131.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 taatgaaattgggttataacttataatccaannnnnnncttttcactagacaatttnnnnnnnntattatagaataaactctattattttaaattttttggagggaattaa taatgaaattgggttataacttataatccaatttttttcttttcactagacaatttaaaaaaaatattatagaataaactctattattttaaattttttggagggaattaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAAAUUGGGUUAUAACUUAUAAUCCAAUUUUUUUCUUUUCACUAGACAAUUUAAAAAAAAUAUUAUAGAAUAAACUCUAUUAUUUUAAAUUUUUUGGAGGGAAUUAA ....((((((((((((((...))))))))))))))....((..(.(((((.(((((((((........(((((......)))))..))))))))).))))).)..)).... (-22.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUUCCCUCCAAAAAAUUUAAAAUAAUAGAGUUUAUUCUAUAAUAUUUUUUUUAAAUUGUCUAGUGAAAAGAAAAAAAUUGGAUUAUAAGUUAUAACCCAAUUUCAUUA ....(((.((......(((((((((.((((.((......))....))))..)))))))))....)).))).......(((((((.(((((...))))).)))))))..... (-12.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 48 6 184 133 NC_003454:FN0419|5end_aspartate_carbamoyltransferase_catalytic_subunit_1059713..1059943_POSITIVE 222 49 8 104 63 NC_003454:FN1519|5end_23S_rRNA_methyltransferase_24792..25022_NEGATIVE 178 39 4 108 76 NC_003454:FN0169|5end_Coproporphyrinogen_III_oxidase_794741..794971_POSITIVE 172 48 8 108 61 NC_003454:FN1605|5end_Adenylosuccinate_synthetase_115276..115506_NEGATIVE 171 55 20 47 14 NC_003454:FN0556|5end_hypothetical_protein_1209000..1209230_NEGATIVE 171 56 25 153 124 NC_003454:FN1913|5end_hydrolase_(HD_superfamily)_411580..411810_NEGATIVE 168 44 7 86 54 NC_003454:FN1480|5end_MG2+_transporter_MGTE_2162663..2162893_NEGATIVE 165 50 11 71 28 NC_003454:FN0299|5end_Aspartyl-tRNA_synthetase_932393..932623_POSITIVE 165 107 79 73 43 NC_003454:FN0185|5end_hypothetical_protein_810469..810699_NEGATIVE 164 102 79 124 103 NC_003454:FN0036|5end_Hypothetical_membrane-spanning_Protein_677609..677839_NEGATIVE 162 80 31 125 68 NC_003454:FN1484|5end_Tetratricopeptide_repeat_family_protein_2167275..2167505_NEGATIVE 161 107 67 40 4 NC_003454:FN0464|5end_hypothetical_protein_1109675..1109905_POSITIVE 160 54 29 28 1 NC_003454:FN1224|5end_2-dehydro-3-deoxyphosphooctonate_aldolase_1883400..1883630_NEGATIVE 160 57 26 111 86 NC_003454:FN0209|5end_Hypothetical_cytosolic_protein_836127..836357_POSITIVE 158 50 23 147 117 NC_003454:FN0979|5end_hypothetical_protein_1632096..1632326_POSITIVE 158 68 28 124 91 NC_003454:FN2087|5end_hypothetical_protein_599719..599949_NEGATIVE 158 106 79 45 7 NC_003454:FN1985|5end_Inner_membrane_protein_488637..488867_NEGATIVE 155 90 67 227 198 NC_003454:FN1266|5end_UTP--glucose-1-phosphate_uridylyltransferase_1923063..1923293_NEGATIVE 155 48 11 109 75 NC_003454:FN1580|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90919..91149_NEGATIVE 154 50 3 83 38 NC_003454:FN0138|5end_Transposase_771238..771468_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 48 6 122 71 NC_003454:FN0418|3end_pyrimidine_regulatory_protein_PyrR_1059731..1059881_POSITIVE 222 49 8 94 53 NC_003454:FN1520|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_24802..24952_NEGATIVE 212 34 2 85 55 NC_003454:FN0161|3end_RNA-directed_DNA_polymerase_789892..790042_POSITIVE 178 39 4 92 60 NC_003454:FN0168|3end_hypothetical_protein_794805..794955_POSITIVE 172 48 8 98 51 NC_003454:FN1606|3end_3-deoxy-D-manno-octulosonic-acid_transferase_115286..115436_NEGATIVE 171 56 25 90 61 NC_003454:FN1914|3end_Anti-sigma_F_factor_antagonist_411643..411793_NEGATIVE 168 44 7 70 38 NC_003454:FN1481|3end_Queuine_tRNA-ribosyltransferase_2162679..2162829_NEGATIVE 165 50 11 52 9 NC_003454:FN0298|3end_Histidyl-tRNA_synthetase_932454..932604_POSITIVE 164 102 79 124 103 NC_003454:FN0037|3end_hypothetical_protein_677609..677759_NEGATIVE 160 54 29 62 35 NC_003454:FN1225|3end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--meso-_lanthionine_ligase_1883366..1883516_NEGATIVE 160 57 26 100 75 NC_003454:FN0208|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase_beta-subunit_836196..836346_POSITIVE 155 48 11 133 99 NC_003454:FN1581|3end_DNA_mismatch_repair_protein_mutS_90895..91045_NEGATIVE 152 50 7 121 61 NC_003454:FN0769|3end_Hemin_transport_system_permease_protein_hmuU_1426752..1426902_POSITIVE 152 51 11 124 88 NC_003454:FN0064|3end_Hypothetical_cytosolic_protein_699922..700072_POSITIVE 151 76 31 98 49 NC_003454:FN0336|3end_hypothetical_protein_969748..969898_NEGATIVE 151 57 26 136 93 NC_003454:FN2076|3end_MunI_regulatory_protein_587536..587686_NEGATIVE 151 109 76 102 62 NC_003454:FN1879|3end_SSU_ribosomal_protein_S20P_367507..367657_POSITIVE 150 59 32 95 71 NC_003454:FN0101|3end_Glutaredoxin_736313..736463_POSITIVE 149 105 68 148 103 NC_003454:FN1042|3end_S1_RNA_binding_domain_1694229..1694379_POSITIVE 148 107 79 145 112 NC_003454:FN1052|3end_hypothetical_protein_1701067..1701217_POSITIVE