Origin IGS: aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttactattcctttttgatataaaaagactgttgcattttaataattaaataagtaaacctaaatatgcaacagctctctttattattttaccttaaatattt Mask Tandem Repeat Region ================================================ aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa Find is-nt database================================================ Query_seq: FN1805:FN1806|FN1805:FN1806:hypothetical protein:Integral membrane protein:->->:287760..287863 104 aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1805:FN1806|FN1805:FN1806:hypothetical protein:Integral membrane protein:->->:287760..287863 104 aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1805:FN1806|FN1805:FN1806:hypothetical protein:Integral membrane protein:->->:287760..287863 104 aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa Predict ORF larger than 30AA ================================================ aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa 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: 83 Start: 61 End: 90 ............................................................TTTGATATAAAAAGACTGTTGCATTTTAAT.............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1805:FN1806|FN1805:FN1806:hypothetical protein:Integral membrane protein:->->:287760..287863 104 aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_003454_FN1805_FN1806|hypothetical protein:Integral membrane protein|POSITIVE:POSITIVE|[287760,287863]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa aaatatttaaggtaaaataataaagagagctgttgcatatttaggtttacttatttaattattaaaatgcaacagtctttttatatcaaaaaggaatagtaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUUUAAGGUAAAAUAAUAAAGAGAGCUGUUGCAUAUUUAGGUUUACUUAUUUAAUUAUUAAAAUGCAACAGUCUUUUUAUAUCAAAAAGGAAUAGUAAAA ...(((((...........(((((((((.(((((((((.(((((..(((......)))...))))))))))))))))))))))).........)))))...... (-21.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUACUAUUCCUUUUUGAUAUAAAAAGACUGUUGCAUUUUAAUAAUUAAAUAAGUAAACCUAAAUAUGCAACAGCUCUCUUUAUUAUUUUACCUUAAAUAUUU ....................(((((.((((((((((((((((...................)))).))))))))).))).)))))................... (-14.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 229 48 9 47 12 NC_003454:FN0424|5end_Dihydroorotate_dehydrogenase_1067119..1067349_POSITIVE 212 50 3 200 147 NC_003454:FN1949|5end_Xaa-Pro_dipeptidase_454922..455152_NEGATIVE 208 82 43 100 59 NC_003454:FN0189|5end_Two-component_response_regulator_yesN_813203..813433_POSITIVE 203 65 25 85 44 NC_003454:FN1983|5end_Alkyl_hydroperoxide_reductase_C22_protein_484619..484849_POSITIVE 199 52 20 221 177 NC_003454:FN1798|5end_Spermidine/putrescine_transport_system_permease_protein_potB_279938..280168_POSITIVE 196 56 22 222 180 NC_003454:FN0300|5end_Iron(III)_dicitrate-binding_protein_934679..934909_POSITIVE 195 88 44 182 131 NC_003454:FN2104|5end_hypothetical_protein_614237..614467_POSITIVE 193 47 3 198 143 NC_003454:FN0799|5end_Isoamylase_1459826..1460056_NEGATIVE 193 46 23 77 57 NC_003454:FN2105|5end_Integral_membrane_protein_614701..614931_POSITIVE 190 58 11 209 157 NC_003454:FN1111|5end_Dipeptide-binding_protein_1756181..1756411_NEGATIVE 189 49 11 44 8 NC_003454:FN0489|5end_Prolipoprotein_diacylglyceryl_transferase_1135425..1135655_NEGATIVE 188 53 23 207 171 NC_003454:FN0938|5end_hypothetical_protein_1591125..1591355_NEGATIVE 185 68 30 180 145 NC_003454:FN0694|5end_S-layer_protein_1350853..1351083_POSITIVE 180 80 64 183 167 NC_003454:FN1257|5end_C4-dicarboxylate_transporter_small_subunit_1913664..1913894_NEGATIVE 178 46 9 36 1 NC_003454:FN0027|5end_hypothetical_protein_664891..665121_NEGATIVE 178 48 4 102 59 NC_003454:FN1512|5end_Phophatidylinositol-4-phosphate_5-kinase_15845..16075_POSITIVE 176 36 1 183 141 NC_003454:FN0310|5end_Iron(III)-transport_ATP-binding_protein_sfuC_945796..946026_POSITIVE 176 50 29 51 30 NC_003454:FN1538|5end_Arsenical_pump-driving_ATPase_52299..52529_NEGATIVE 173 70 27 127 79 NC_003454:FN1310|5end_TonB_protein_1965876..1966106_NEGATIVE 173 50 24 220 194 NC_003454:FN0165|5end_hypothetical_protein_793491..793721_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 38 10 63 30 NC_003454:FN0212|3end_hypothetical_protein_837583..837733_NEGATIVE 229 87 55 72 35 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 220 48 10 35 1 NC_003454:FN0423|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1067187..1067337_POSITIVE 213 63 23 95 45 NC_003454:FN1006|3end_Acetyltransferase_1660998..1661148_NEGATIVE 213 80 31 82 43 NC_003454:FN1907|3end_Thymidylate_synthase_400546..400696_POSITIVE 212 50 3 59 6 NC_003454:FN1950|3end_Serine_protease_455063..455213_NEGATIVE 211 51 24 43 18 NC_003454:FN0340|3end_Hypothetical_membrane-spanning_Protein_972638..972788_NEGATIVE 208 82 43 69 28 NC_003454:FN0188|3end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_813252..813402_POSITIVE 206 37 19 29 11 NC_003454:FN0339|3end_hypothetical_protein_972588..972738_POSITIVE 205 86 57 96 65 NC_003454:FN0029|3end_Flavodoxin_666596..666746_NEGATIVE 204 82 53 79 49 NC_003454:FN0026|3end_Hypothetical_exported_24-amino_acid_repeat_protein_664832..664982_POSITIVE 204 89 44 66 30 NC_003454:FN1508|3end_3,4-dihydroxy-2-butanone-4-phosphate_synthase_14117..14267_POSITIVE 198 78 38 80 33 NC_003454:FN1428|3end_Branched-chain_amino_acid_transport_ATP-binding_protein_livF_2096860..2097010_NEGATIVE 196 81 44 85 55 NC_003454:FN0532|3end_Hypothetical_membrane-spanning_protein_1186524..1186674_NEGATIVE 195 86 57 96 63 NC_003454:FN1340|3end_Glutamyl-tRNA_synthetase_1993353..1993503_NEGATIVE 195 88 44 74 23 NC_003454:FN2103|3end_RecA_protein_614209..614359_POSITIVE 194 43 1 59 21 NC_003454:FN0636|3end_hypothetical_protein_1295609..1295759_POSITIVE 193 47 3 77 22 NC_003454:FN0800|3end_Amino_acid-binding_protein_1459947..1460097_NEGATIVE 193 46 23 56 36 NC_003454:FN2104|3end_hypothetical_protein_614760..614910_POSITIVE 192 37 9 61 24 NC_003454:FN1005|3end_hypothetical_protein_1660975..1661125_POSITIVE