Origin IGS: agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tattttcctcctcttatggattttataaaaactttattcttattctatcgttgattgatagttatgtcaagccttttatgtatttttctctttaaattttcttaaaaaatacattttgtagatttattgtactaaattaataaagtattttatttttactaattatgatataataataaaatcaaaggagtgattcaaaagct Mask Tandem Repeat Region ================================================ agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata Find is-nt database================================================ Query_seq: FN0782:FN0783|FN0782:FN0783:Methyltransferase:Acyl-CoA dehydrogenase:<-->:1439103..1439305 203 agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0782:FN0783|FN0782:FN0783:Methyltransferase:Acyl-CoA dehydrogenase:<-->:1439103..1439305 203 agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0782:FN0783|FN0782:FN0783:Methyltransferase:Acyl-CoA dehydrogenase:<-->:1439103..1439305 203 agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata Predict ORF larger than 30AA ================================================ agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata 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: 91 Start: 133 End: 162 ....................................................................................................................................CTTGACATAACTATCAATCAACGATAGAAT......................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 5 End: 34 ....TTTGAATCACTCCTTTGATTTTATTATTAT......................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0782:FN0783|FN0782:FN0783:Methyltransferase:Acyl-CoA dehydrogenase:<-->:1439103..1439305 203 agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: NC_003454_FN0782_FN0783|Methyltransferase:Acyl-CoA dehydrogenase|NEGATIVE:POSITIVE|[1439103,1439305]|203 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata agcttttgaatcactcctttgattttattattatatcataattagtaaaaataaaatactttattaatttagtacaataaatctacaaaatgtattttttaagaaaatttaaagagaaaaatacataaaaggcttgacataactatcaatcaacgatagaataagaataaagtttttataaaatccataagaggaggaaaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUUUGAAUCACUCCUUUGAUUUUAUUAUUAUAUCAUAAUUAGUAAAAAUAAAAUACUUUAUUAAUUUAGUACAAUAAAUCUACAAAAUGUAUUUUUUAAGAAAAUUUAAAGAGAAAAAUACAUAAAAGGCUUGACAUAACUAUCAAUCAACGAUAGAAUAAGAAUAAAGUUUUUAUAAAAUCCAUAAGAGGAGGAAAAUA ..........((.(((((((((((((((((((.(((...((((((((((..........))))))))))..))).))))).........(((((((((((...............))))))))))).((((((((.......(((((.......)))))..........)))))))).)))))))....)))))))))..... (-31.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUUCCUCCUCUUAUGGAUUUUAUAAAAACUUUAUUCUUAUUCUAUCGUUGAUUGAUAGUUAUGUCAAGCCUUUUAUGUAUUUUUCUCUUUAAAUUUUCUUAAAAAAUACAUUUUGUAGAUUUAUUGUACUAAAUUAAUAAAGUAUUUUAUUUUUACUAAUUAUGAUAUAAUAAUAAAAUCAAAGGAGUGAUUCAAAAGCU .....(((((((......((((((((..................((((((.....))))))((((((((........((((((((((.................))))))))))...(((((..((..(((((..........)))))..))..)))))......))))))))..))))))))..))))).)).......... (-34.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 655 50 1 141 92 NC_003454:FN0782|5end_Methyltransferase_1439012..1439242_NEGATIVE 236 35 1 118 78 NC_003454:FN1084|5end_hypothetical_protein_1728661..1728891_POSITIVE 219 58 14 145 98 NC_003454:FN0607|5end_metal_dependent_phosphohydrolase_1261564..1261794_POSITIVE 218 38 2 123 87 NC_003454:FN1741|5end_ATP_synthase_subunit_I_240477..240707_NEGATIVE 189 54 13 46 13 NC_003454:FN0064|5end_Hypothetical_cytosolic_protein_699489..699719_POSITIVE 188 160 143 29 12 NC_003454:FN1232|5end_Transcriptional_regulator,_MarR_family_1889341..1889571_NEGATIVE 188 193 156 200 164 NC_003454:FN1895|5end_hypothetical_protein_382871..383101_NEGATIVE 186 46 1 139 83 NC_003454:FN0240|5end_Thymidylate_synthase_863894..864124_POSITIVE 185 51 14 142 100 NC_003454:FN1444|5end_GMP_synthase_[glutamine-hydrolyzing]_2111585..2111815_POSITIVE 177 41 11 132 95 NC_003454:FN1975|5end_ATP-dependent_RNA_helicase_475599..475829_POSITIVE 175 49 10 139 93 NC_003454:FN1038|5end_Transporter_1690075..1690305_POSITIVE 173 29 5 106 82 NC_003454:FN1095|5end_hypothetical_protein_1740232..1740462_POSITIVE 166 40 1 231 186 NC_003454:FN0677|5end_hypothetical_protein_1332641..1332871_POSITIVE 165 41 3 44 10 NC_003454:FN1401|5end_urocanate_hydratase_2058592..2058822_POSITIVE 165 160 118 163 131 NC_003454:FN0173|5end_hypothetical_protein_797839..798069_POSITIVE 165 45 3 87 48 NC_003454:FN1605|5end_Adenylosuccinate_synthetase_115276..115506_NEGATIVE 164 43 1 136 96 NC_003454:FN1033|5end_Methyltransferase_1687545..1687775_NEGATIVE 164 60 14 144 100 NC_003454:FN0015|5end_hypothetical_protein_653500..653730_NEGATIVE 163 98 68 76 47 NC_003454:FN0979|5end_hypothetical_protein_1632096..1632326_POSITIVE 160 48 1 66 7 NC_003454:FN1326|5end_Undecaprenyl_pyrophosphate_synthetase_1981890..1982120_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 218 38 2 136 100 NC_003454:FN1742|3end_V-type_sodium_ATP_synthase_subunit_G_240464..240614_NEGATIVE 217 39 2 107 63 NC_003454:FN1515|3end_Phophatidylinositol-4-phosphate_5-kinase_20652..20802_POSITIVE 186 46 1 88 32 NC_003454:FN0239|3end_hypothetical_protein_863923..864073_POSITIVE 178 199 163 45 7 NC_003454:FN1460|3end_Hypothetical_cytosolic_protein_2141682..2141832_POSITIVE 165 160 118 49 17 NC_003454:FN0172|3end_RNA_binding_protein_797805..797955_POSITIVE 165 45 3 77 38 NC_003454:FN1606|3end_3-deoxy-D-manno-octulosonic-acid_transferase_115286..115436_NEGATIVE 163 134 93 52 1 NC_003454:FN0514|3end_hypothetical_protein_1163912..1164062_POSITIVE 163 196 158 149 107 NC_003454:FN0495|3end_Acetyl-CoA_acetyltransferase_1140855..1141005_POSITIVE 161 47 1 112 65 NC_003454:FN0109|3end_hypothetical_protein_744333..744483_NEGATIVE 159 190 149 83 46 NC_003454:FN0214|3end_Crossover_junction_endodeoxyribonuclease_ruvC_838668..838818_NEGATIVE 158 47 2 112 65 NC_003454:FN0973|3end_Histidinol-phosphate_aminotransferase_1625626..1625776_NEGATIVE 158 37 1 105 68 NC_003454:FN0118|3end_Chaperone_protein_dnaJ_752156..752306_POSITIVE 157 145 101 81 39 NC_003454:FN0457|3end_hypothetical_protein_1103803..1103953_POSITIVE 155 23 1 39 19 NC_003454:FN0526|3end_Florfenicol_resistance_protein_1181901..1182051_NEGATIVE 155 70 23 86 25 NC_003454:FN1867|3end_Zn-dependent_alcohol_dehydrogenase_and_related_dehydrogenase_358560..358710_NEGATIVE 153 60 26 58 22 NC_003454:FN1289|3end_hypothetical_protein_1944732..1944882_NEGATIVE 151 151 121 62 34 NC_003454:FN1450|3end_Integral_membrane_protein_2130004..2130154_NEGATIVE 150 161 127 63 36 NC_003454:FN1340|3end_Glutamyl-tRNA_synthetase_1993353..1993503_NEGATIVE 150 161 127 44 17 NC_003454:FN0528|3end_Cold_shock_protein_1184746..1184896_POSITIVE 150 161 127 40 13 NC_003454:FN0371|3end_hypothetical_protein_1000840..1000990_POSITIVE