Origin IGS: aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggatagagatttccccttagcttttgcaaacttgccaggaattatttttggattaatagctgcatttacagcaatgtaatacaaattaaaaagagattattataaatttttttctttataataatctcttttt Mask Tandem Repeat Region ================================================ aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt Find is-nt database================================================ Query_seq: FN0586:FN0587|FN0586:FN0587:Two-component sensor kinase czcS:Hypothetical membrane-spanning protein:-><-:1241918..1242052 135 aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0586:FN0587|FN0586:FN0587:Two-component sensor kinase czcS:Hypothetical membrane-spanning protein:-><-:1241918..1242052 135 aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0586:FN0587|FN0586:FN0587:Two-component sensor kinase czcS:Hypothetical membrane-spanning protein:-><-:1241918..1242052 135 aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt Predict ORF larger than 30AA ================================================ aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt 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================================================ aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0586:FN0587|FN0586:FN0587:Two-component sensor kinase czcS:Hypothetical membrane-spanning protein:-><-:1241918..1242052 135 aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: NC_003454_FN0586_FN0587|Two-component sensor kinase czcS:Hypothetical membrane-spanning protein|POSITIVE:NEGATIVE|[1241918,1242052]|135 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 aaaaagagattattataaagnnnnnnntttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt aaaaagagattattataaagaaaaaaatttataataatctctttttaatttgtattacattgctgtaaatgcagctattaatccaaaaataattcctggcaagtttgcaaaagctaaggggaaatctctatcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGAGAUUAUUAUAAAGAAAAAAAUUUAUAAUAAUCUCUUUUUAAUUUGUAUUACAUUGCUGUAAAUGCAGCUAUUAAUCCAAAAAUAAUUCCUGGCAAGUUUGCAAAAGCUAAGGGGAAAUCUCUAUCCUU (((((((((((((((((((........)))))))))))))))))))..((((.((((....(((((....)))))...)))).)))).....(((((....(((((....)))))..)))))............. (-35.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGAUAGAGAUUUCCCCUUAGCUUUUGCAAACUUGCCAGGAAUUAUUUUUGGAUUAAUAGCUGCAUUUACAGCAAUGUAAUACAAAUUAAAAAGAGAUUAUUAUAAAUUUUUUUCUUUAUAAUAAUCUCUUUUU ..(((........))).........(((((......((((((.....)))))).......((((......))))..)))))........(((((((((((((((((((........))))))))))))))))))) (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 80 32 75 23 NC_003454:FN0251|5end_Hypothetical_membrane-spanning_Protein_873796..874026_POSITIVE 334 80 32 75 23 NC_003454:FN2061|5end_Hypothetical_membrane-spanning_protein_574046..574276_NEGATIVE 334 80 32 75 23 NC_003454:FN2050|5end_Hypothetical_membrane-spanning_protein_559970..560200_NEGATIVE 244 98 51 114 66 NC_003454:FN2121|5end_Hypothetical_exported_24-amino_acid_repeat_protein_629728..629958_NEGATIVE 237 127 92 169 140 NC_003454:FN0887|5end_Oligoendopeptidase_F_1549711..1549941_NEGATIVE 220 74 38 36 2 NC_003454:FN1472|5end_N-acetylneuraminate-binding_protein_2154025..2154255_POSITIVE 220 122 88 39 3 NC_003454:FN1256|5end_C4-dicarboxylate_transporter_large_subunit_1913206..1913436_NEGATIVE 206 50 1 222 169 NC_003454:FN1949|5end_Xaa-Pro_dipeptidase_454922..455152_NEGATIVE 204 105 63 189 155 NC_003454:FN1283|5end_DNA-directed_RNA_polymerase_alpha_subunit_1942675..1942905_NEGATIVE 204 77 35 140 102 NC_003454:FN1089|5end_hypothetical_protein_1733042..1733272_POSITIVE 203 80 38 59 6 NC_003454:FN1005|5end_hypothetical_protein_1660422..1660652_POSITIVE 201 110 65 51 1 NC_003454:FN0395|5end_Transporter_1033106..1033336_POSITIVE 200 114 73 156 120 NC_003454:FN1627|5end_SSU_ribosomal_protein_S5P_133556..133786_NEGATIVE 196 97 56 74 34 NC_003454:FN0711|5end_Phosphopantothenate--cysteine_ligase_1369569..1369799_POSITIVE 195 85 49 165 122 NC_003454:FN0659|5end_ABC_transporter_permease_protein_1316391..1316621_NEGATIVE 195 85 51 229 193 NC_003454:FN1725|5end_Potassium_uptake_protein_KtrB_224671..224901_NEGATIVE 192 121 82 146 112 NC_003454:FN2038|5end_LSU_ribosomal_protein_L10P_547696..547926_NEGATIVE 188 84 53 52 14 NC_003454:FN0083|5end_Ethanolamine_utilization_protein_eutM_precursor_721180..721410_POSITIVE 188 97 61 158 119 NC_003454:FN2110|5end_Hypothetical_exported_24-amino_acid_repeat_protein_622330..622560_NEGATIVE 187 46 1 195 155 NC_003454:FN0607|5end_metal_dependent_phosphohydrolase_1261564..1261794_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 46 1 90 45 NC_003454:FN0586|3end_Two-component_sensor_kinase_czcS_1241857..1242007_POSITIVE 220 98 61 44 4 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 211 46 1 80 28 NC_003454:FN1008|3end_hypothetical_protein_1662528..1662678_NEGATIVE 206 50 1 81 28 NC_003454:FN1950|3end_Serine_protease_455063..455213_NEGATIVE 205 122 106 24 8 NC_003454:FN1257|3end_C4-dicarboxylate_transporter_small_subunit_1913221..1913371_NEGATIVE 204 77 35 113 75 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE 200 114 73 132 96 NC_003454:FN1628|3end_LSU_ribosomal_protein_L18P_133580..133730_NEGATIVE 196 127 92 146 118 NC_003454:FN1287|3end_Bacterial_Protein_Translation_Initiation_Factor_1_(IF-1)_1944415..1944565_NEGATIVE 196 97 56 57 17 NC_003454:FN0710|3end_hypothetical_protein_1369632..1369782_POSITIVE 195 119 92 146 125 NC_003454:FN0888|3end_Uracil_permease_1549726..1549876_NEGATIVE 188 97 61 54 15 NC_003454:FN2111|3end_Hypothetical_exported_24-amino_acid_repeat_protein_622434..622584_NEGATIVE 187 46 1 70 30 NC_003454:FN0606|3end_Translation_initiation_inhibitor_1261519..1261669_POSITIVE 187 85 47 139 94 NC_003454:FN1592|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_D_103162..103312_NEGATIVE 185 76 34 118 69 NC_003454:FN0049|3end_hypothetical_protein_686919..687069_POSITIVE 184 63 25 116 68 NC_003454:FN1391|3end_Acetyltransferase_2049133..2049283_POSITIVE 184 97 51 90 42 NC_003454:FN1670|3end_Choline_kinase_166470..166620_NEGATIVE 182 50 5 69 28 NC_003454:FN0310|3end_Iron(III)-transport_ATP-binding_protein_sfuC_946946..947096_POSITIVE 179 104 61 63 23 NC_003454:FN0183|3end_Glycerol-3-phosphate_dehydrogenase_807078..807228_NEGATIVE 176 115 73 115 67 NC_003454:FN1730|3end_Anthranilate_synthase_component_I_229081..229231_NEGATIVE 174 78 38 46 6 NC_003454:FN1538|3end_Arsenical_pump-driving_ATPase_51109..51259_NEGATIVE