Origin IGS: aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagatttattattttttgtaataaatgttagatatattttactcctctctagctgattgaaaggatttttttaaatcttcaatcagctttttttgttaataaaatataaataatgttataatagtaacaagagataaattttaaggaggaaatttt Mask Tandem Repeat Region ================================================ aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt Find is-nt database================================================ Query_seq: FN1732:FN1733|FN1732:FN1733:hypothetical protein:ATP synthase subunit D:<-<-:232169..232325 157 aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1732:FN1733|FN1732:FN1733:hypothetical protein:ATP synthase subunit D:<-<-:232169..232325 157 aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1732:FN1733|FN1732:FN1733:hypothetical protein:ATP synthase subunit D:<-<-:232169..232325 157 aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt Predict ORF larger than 30AA ================================================ aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt 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================================================ aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -6.5 Tail_Score: -5.84381 Start: 70 End: 105 Full_Region: ttttactcctctcta gctgattgaaaggattt tttt aaatcttcaatcagc tttttttgttaataa .....................................................................gctgattgaaaggatttttttaaatcttcaatcagc.................................................... Find igs database================================================ Query_seq: FN1732:FN1733|FN1732:FN1733:hypothetical protein:ATP synthase subunit D:<-<-:232169..232325 157 aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_003454_FN1732_FN1733|hypothetical protein:ATP synthase subunit D|NEGATIVE:NEGATIVE|[232169,232325]|157 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacnnnnnnngctgattgaagatttnnnnnnntcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt aaaatttcctccttaaaatttatctcttgttactattataacattatttatattttattaacaaaaaaagctgattgaagatttaaaaaaatcctttcaatcagctagagaggagtaaaatatatctaacatttattacaaaaaataataaatcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUCCUCCUUAAAAUUUAUCUCUUGUUACUAUUAUAACAUUAUUUAUAUUUUAUUAACAAAAAAAGCUGAUUGAAGAUUUAAAAAAAUCCUUUCAAUCAGCUAGAGAGGAGUAAAAUAUAUCUAACAUUUAUUACAAAAAAUAAUAAAUCUUU ....(((.((((((............((((((.((.(((((......)))))...)).))))))....((((((((((((((((....)))))..)))))))))))...)))))).)))...........((((((((.......)))))))).... (-31.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAUUUAUUAUUUUUUGUAAUAAAUGUUAGAUAUAUUUUACUCCUCUCUAGCUGAUUGAAAGGAUUUUUUUAAAUCUUCAAUCAGCUUUUUUUGUUAAUAAAAUAUAAAUAAUGUUAUAAUAGUAACAAGAGAUAAAUUUUAAGGAGGAAAUUUU .((.(((((((((.....))))))))).)).............((((((..((((((((((..((((((....))))))))))))))))((((((((((......(((((......)))))....))))))))))..........))))))...... (-38.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 756 120 71 211 162 NC_003454:FN1732|5end_hypothetical_protein_232078..232308_NEGATIVE 230 50 5 191 147 NC_003454:FN1177|5end_hypothetical_protein_1838805..1839035_NEGATIVE 230 41 1 185 143 NC_003454:FN0688|5end_hypothetical_protein_1344068..1344298_POSITIVE 230 45 3 136 92 NC_003454:FN0062|5end_Hypothetical_cytosolic_protein_698605..698835_POSITIVE 217 50 5 193 148 NC_003454:FN0689|5end_hypothetical_protein_1344658..1344888_POSITIVE 213 106 63 159 122 NC_003454:FN0078|5end_Ethanolamine_utilization_protein_eutA_716205..716435_POSITIVE 210 39 8 132 98 NC_003454:FN1085|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme_1728934..1729164_POSITIVE 205 50 5 172 130 NC_003454:FN1155|5end_Cell_division_protein_ftsI_1809442..1809672_POSITIVE 204 49 5 136 94 NC_003454:FN0150|5end_Acyl_carrier_protein_778453..778683_POSITIVE 191 99 63 153 115 NC_003454:FN1103|5end_Excinuclease_ABC_subunit_A_1746559..1746789_POSITIVE 188 44 8 63 17 NC_003454:FN1101|5end_ATPase_1744547..1744777_POSITIVE 188 138 96 185 140 NC_003454:FN0355|5end_S-adenosylmethionine_synthetase_987227..987457_NEGATIVE 183 136 93 70 33 NC_003454:FN0147|5end_fatty_acid/phospholipid_synthesis_protein_775462..775692_POSITIVE 179 84 41 211 170 NC_003454:FN1448|5end_Hypothetical_cytosolic_protein_2118428..2118658_NEGATIVE 179 114 76 220 184 NC_003454:FN0319|5end_Citrate_(pro-3S)-lyase_ligase_956855..957085_NEGATIVE 177 44 5 148 104 NC_003454:FN1000|5end_biotin_synthase_1654939..1655169_POSITIVE 176 36 2 138 92 NC_003454:FN1966|5end_hypothetical_protein_465377..465607_NEGATIVE 174 22 4 110 92 NC_003454:FN1306|5end_Methyltransferase_1961674..1961904_POSITIVE 174 121 93 40 6 NC_003454:FN0527|5end_Alanyl-tRNA_synthetase_1184098..1184328_NEGATIVE 174 25 4 223 203 NC_003454:FN2113|5end_hypothetical_protein_623932..624162_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 41 1 83 41 NC_003454:FN0687|3end_hypothetical_protein_1344046..1344196_POSITIVE 225 49 3 96 46 NC_003454:FN1954|3end_Glycerophosphoryl_diester_phosphodiesterase_459777..459927_NEGATIVE 217 50 5 64 19 NC_003454:FN0688|3end_hypothetical_protein_1344609..1344759_POSITIVE 213 106 63 46 9 NC_003454:FN0077|3end_Ethanolamine_two-component_sensor_kinase_716172..716322_POSITIVE 210 39 8 116 82 NC_003454:FN1084|3end_hypothetical_protein_1728998..1729148_POSITIVE 204 49 5 68 26 NC_003454:FN0149|3end_Malonyl-CoA-[acyl-carrier-protein]_transacylase_778465..778615_POSITIVE 194 49 5 151 110 NC_003454:FN1154|3end_Ribonuclease_BN_1809502..1809652_POSITIVE 191 99 63 85 47 NC_003454:FN1102|3end_tRNA_2'phosphotransferase_1746571..1746721_POSITIVE 190 136 92 147 99 NC_003454:FN1516|3end_hypothetical_protein_20664..20814_NEGATIVE 186 104 64 82 44 NC_003454:FN0315|3end_Transcriptional_regulator,_AraC_family_952859..953009_POSITIVE 179 49 6 100 65 NC_003454:FN1294|3end_Ribosomal-protein-alanine_acetyltransferase_1952517..1952667_NEGATIVE 178 150 103 62 19 NC_003454:FN0844|3end_hypothetical_protein_1503774..1503924_POSITIVE 177 120 91 82 55 NC_003454:FN1674|3end_hypothetical_protein_172225..172375_POSITIVE 176 36 2 62 16 NC_003454:FN1967|3end_hypothetical_protein_465453..465603_NEGATIVE 174 25 4 145 125 NC_003454:FN2114|3end_hypothetical_protein_624010..624160_NEGATIVE 173 45 8 40 1 NC_003454:FN0061|3end_Thermostable_carboxypeptidase_1_698589..698739_POSITIVE 172 40 7 63 27 NC_003454:FN0245|3end_Copper-exporting_ATPase_870680..870830_POSITIVE 172 47 1 57 18 NC_003454:FN1588|3end_hypothetical_protein_99797..99947_POSITIVE 171 67 33 113 69 NC_003454:FN1109|3end_Dipeptide_transport_ATP-binding_protein_dppF_1752994..1753144_NEGATIVE 168 49 7 80 31 NC_003454:FN1239|3end_hypothetical_protein_1896403..1896553_NEGATIVE